Some comments:
1) Are you picking up car rental from airport ?

2) #2 Lake Toya to Otaru is about 2.5 hours drive, earliest you reach there will be late morning. Then you walk around/eat/etc. Then you need to rush from Otaru to Asahikawa is another 2.5-3 hours drive and check-in by 3-5pm as that's their acceptable time, late check in (6pm or later) is sort of frowned upon even if you inform the host. Hokkaido is sort of laid back and close early, as compared to Honshu. My suggestion is try to over night somewhere (maybe Otaru) and enjoy. I think Otaru can spend 4-6 hours walk, cafe, relax, etc. for me. Some people say 2 hours all done

3) Furano - Tomamu - Sapporo is the longest drive. To and fro you may spend 5-6 hours on the road. Normally I suggest to spend minimum 2 nights if you go that far and enjoy the journey + environment there. Don't just rush along the expressway, try stop by those rest area or nearby towns for interesting stuff/food/local produce/etc. e.g. white/yellow corn, melons, apricots, etc. depending on season maybe cheaper.

4) When and where will you return your car rental ? My first and this question is because you don't really need to drive in Sapporo, you can get around with subway and buses, and it is not easy & cheap to find car park in Sapporo city centre. During summer, they have food & beer fest along the whole Odori park.

2) Lake Toya daily fireworks ... emm ... *spoiler alert* how to say as not to disappoint you ... it isn't that spectacular as those New Year countdown even in places like KLCC/DPC/Sunway/Genting. Just to set your expectation.
On the way from Noboribetsu to Lake Toya, you'll pass by several fruit farms or vegetables if you intend to cook or steamboat, actually the local produce in Hokkaido are very good and our next trip is to cook/steamboat ourselves at several homestay places.

For me, Otaru can spend the daylight times to walk around and eat/drink along the inner street. Once 6pm and sky gets dark, 80% of the tourist will be gone and you can have more room to breathe and enjoy the view. Also it's the time to walk along the canal with lights and maybe have dinner also. Summer is nice also, it won't be smelly or dirty like our Klang/Gombak river.

Then you can arrange next day wake up earlier and drive straight to Asahikawa so you'll have few more hours there to spend and adjust your Asahikawa/Biei/Furano schedule.

3) I've not yet been to Tomamu, but drove further to Abashiri - Shari. Maybe I'm not that young anymore, so our schedule are like half day itenary, another half day just wander around town/local, or relax at the homestay. My suggestion is no need spend too many days shopping in Sapporo. Shopping maybe another trip to Tokyo/Osaka, those places are better. Of course there are some stuff which are available in Hokkaido or season-based only.
So for me is a definite yes to spend +1 day in either Asahikawa/Biei/Furano or somewhere Tomamu.

My fav Marusei Butter Sandwich and I think you are quite near the Obihiro factory somewhere near Tomamu.

4) Yes, as long as you can walk a lot, if you walk Dotonburi before, you will make it in Sapporo city centre. Even in Sapporo JR station and underground shopping, there are many surprise temporary kiosk/stalls depending on season or some local produce shops. Same in other cities like Furano/Biei/Asahikawa/etc.

Not sure if you have finalised your schedule or not, but after thinking a bit, may I give two suggestions:
A) Chitose airport - Lake Toya - Asahikawa/Biei/Furano/Tomamu - Sapporo drop luggage - return car - take train to Otaru

B) Chitose airport - Asahikawa/Biei/Furano/Tomamu - Lake Toya - Sapporo drop luggage - return car - take train to Otaru - Sapporo

Otaru no need overnight, all luggage at Sapporo for the last few days. You can take the late evening train from Otaru -> Sapporo

I prefer option B, remember Noboribetsu you can dip your leg into river onsen ? After walking many days, can relax there. Also, cover the long distance first to reduce the overall risk.

You still can drive to Otaru and return car late by 1 day. Where you plan to return car ? Airport/Sapporo city ? Cause I know mostly will have some surcharge if you don't return to the same location.

Also, you may think about repack and store few luggages at airport when return car, they have a limit like 48-72 hours storage. So at your last day, I'm sure with additional luggage from shopping/souvenirs/snacks, you don't have to drag so many luggages from airbnb to train station. Additional cost involve here.

The butter sandwich, you can get the plain transparent plastic packing which is cheapest per piece for own consumption at Furano (which I know, I'm sure somewhere else also got, but not in Sapporo city). Those paper wrap nicely are for gifts but more expensive, price is fixed everywhere, remember get GST refund.

Same with Shiroi Koibito, use calculator to find cheapest per piece for 12/18/21/24/36/48 packaging price fixed everywhere.

Some shops may put cheaper price, but that is without GST included. In the end, same same.

With your pass, why you want to ride Limited Express when you can ride the Sanyo Shinkansen train between Shin-Osaka <> Hiroshima ?

But of course, to answer your question: Yes.

You can ride Ordinary Car - Non Reserved (look at the train platform to queue properly) without additional fare.

oic, since you are nearby, try check out Kinosaki Onsen. BTW, I just notice you may take the same train I took, Kinosaki/Konotori. As answered above, yes can ride limited express non-reserve seat without additional fare.

You need to switch trains at Daikokucho Station from Midosuji Line (red) to Yotsubashi Line (blue). Both trains could be running same direction at the same platform (or another platform), you need to do further checking.

Once you reach Higobashi station (blue Yotsubashi line), then only you get out of station and walk to hotel.

Short answer: Technically no need exit.

Long answer: There is Fare Adjust machine at Kyoto station and some other stations, else goto Customer Service counter at wherever your final exit. If your journey doesn't need to pay anything, then no need adjust fare. i.e. top-up some credit into your Haruka ticket or ICOCA card.

Bear in mind, it may auto activate your X days free pass or whatever combo ticket you purchase. Normally what I do is at KIX JR Office, collect all booked tickets and ask them to confirm and hardcode all the dates for the passes, etc. at the counter and pay for it.

Should be more than enough, for my transit (ANA) in NRT, clearing immigration is quite efficient (Japanese style), pick up luggage, exit customs, but don't exit arrival hall. There is a small door for "transit" , go there, show boarding pass, drop luggage and goto domestic gate.

oh, probably mine is slightly different. I'm ANA all the way KUL-NRT-CTS, so 2x boarding pass printed in KLIA. I presume you are flying different airlines ?

Used 3x TravelRecommends. 2x in Japan. No issue with data, I sync photos & videos to Google Drive/Photos, update AppStore apps, etc. several GB/day. shared between 4x. Only thing is generally the battery lasts about half a day only, so bring your own powerbank or plug into your rental car. Bring cigarette adapter USB in case some cars doesn't has USB port.

Unlikely rental car will break down in Japan. Just prepare your Maxis/Celcom/Digi/etc. roaming will do. Or you can ask rental if can whatsapp/line/etc. Very good coverage in Hokkaido. Only two small locations that doesn't have signal I have encountered. The sulfur pit at very top of Asahidake and the waterfall at the gorge near Shiretoko.

I can advise on KUL-Narita-Itami. Refer few pages back, I was transit ANA from KUL-Narita-Chitose. Immigration at Narita, pickup all luggage, once exit Customs, don't goto arrival hall (Narita) there is a small door for domestic transfer. Drop your luggage there, and walk to domestic terminal. I have my 2x boarding pass printed in KLIA, just show them.

Once arrive at final destination you are treated like domestic passenger already. No more immigration/customs.

Yes, Narita is you travel in as International, hence passport and customs. Once that is done, you considered "in" already and just transfer to domestic terminal/flight. Since 2nd flight is not international-connecting-flight, you need to take all your luggages to pass through customs. No need check-in or goto transfer counter, if you have 2x boarding pass (ANA) printed at KLIA.

2.5 hours is more than enough for Narita transit, with Japanese efficiency (not bodek, but that's the reality), you probably clear everything and at domestic terminal boarding gate within 1 hour.

However, don't take things for granted just as most of us say so. Better go straight than walk around here and there.

I guess part of it could be due to the earthquake and people scare to travel in recent times. That's what my travel partners say when we discuss/plan for our upcoming trip.

Tokyo / Sapporo/Otaru can take rail.

Asahikawa/Biei/Furano/Noboribetsu and return car at Hakodate - I prefer to rent car for this route.

I would say depends on individual, some can stand cold, some in KL also wear jacket and walk under the sun.

But my advise is bring a sweater/fleece/turtle-neck in your backpack. Get a medium size ziplock bag from Daiso to squeeze out all the air.

Worst case scenario, your luggage is missing/delayed. Imagine if you can withstand the temperature to go from airport to hotel and go out for meals/shopping. e.g. queue at bus/taxi stand, walk from station to hotel, etc.