Yamaha XMax 250 also a good scooter.

Yes but the size is bigger & heavier.

And so is Benelli.

If you are not looking at Chinese bikes and scooters ...you have definitely pigeon holed yourself.

You can't buy a new versys 250. Because there are none....until modenas decides to bring them in again.

So that leaves the KTM. But if you are worried about parts and reliability, you are pretty much left with no candidates. Small displacement KTM are coming out if India, while the bigger 790 is coming out if china.

There are no problems with parts for modenas/Bajaj bikes. Basically they are the poor man's KTM. (Yes you read that right. Bajaj makes KTMs). But judging from your preferences, the Bajaj based bikes probably aren't for you either.
If based on your initial preferences of a city bike with comfy seat, only a scoot fits the bill. Even a small adventure bike is big  if your previous experience is a 100kg kapchai, any of the 250 ADVs and maxi 250s will be close to double that.

The closest 250 scoot that fits your bill would be the ES250 scoot..but that being a Chinese bikes and a scooter...no dice.

Bajaj Pulsar is Indian being sold in here as a rebadged Modenas bike.

Yes, you will run into some QC issues (typical of India manufacturing, made worse by Modenas) but spare parts and maintenance in general is dirt cheap. In my experience, I have had the rear brake go kaput right out of factory, rear pillion seat not being able to lock up tight, and minor fork leaking, all of which can be covered by warranty or you can fix on the cheap for less than 300 if you wish to avoid DRB-HICOM's warranty shenanigans. If you are careful you can get to Penang mainland on a single tank from Petronas at Sg Buloh Overhead Bridge.

If you don't want a Yamaha FZ150 or just want the cheapest ABS bike you can buy, this is pretty much the most economical alternative. As long as you are staying in Klang Valley there are several specialists covering key areas, the ones I know are in Kota Damansara, Selayang, and Puchong Prima. There are other normal service centers that service other bikes like Eang Chun in Wangsa Maju that will keep spare parts for the bike as well.

KTM ADV 250 is heavy, you are approaching 180kg with that thing and is tall, but is plenty comfortable. Price however will make your wallet cry and costs just 1-2k below the Honda CBR250RR.

Personally have never tried Versys 250 so can't say anything about it other than it shouldn't give you any major issues, considering its based on a very old reliable Kawa design.

Another alternative you can consider is to buy a used Kawasaki Z250 and modify the rear seat to have better padding.

Is better padding for the rear seat the only mod I can make? Might be a stupid question, but are there aftermarket seats that are larger?

The thing about Benelli is that it's an Italian brand owned by a Chinese company. I am willing to trust Italian design w/ Chinese manufacturing over Chinese design w/ Chinese manufacturing.

I don't mind getting used bikes, so no new Versys 250s isn't that much of an issue for me aside from possibly making used ones more expensive than they would otherwise be.

For Modenas/Bajaj, I'm not worried about possible lack of parts. Someone has already mentioned QC issues and having to bring theirs to the shop for repair & replacement. I can't deal with that when whichever bike I buy will be my only mode of transport besides Grab or public transport.

If the Versys 250 isn't an option for whatever reason I might just go for the Kawasaki Z250 like one or two other people have recommended.

True..But this scooter has the extra power for two up riding. Furthermore can use its extra size and power for touring and not just city commute.

TS says most of the time will be two up. The extra space and power is welcomed. Size, after a while sure can handle.

Is better padding for the rear seat the only mod I can make? Might be a stupid question, but are there aftermarket seats that are larger?