huh? which area?

i thought this is common in every other countries?

of coz, it MIGHTTTT happen if u go do their market or what not la..if u go to those restaurants, cafes, malls, everyhting got fixed price d how to cheat you

Some small comments;

Day 2 is freaking packed, if you're gonna go from Hongdae to Lotte Tower which I'm pretty sure would already be late evening if not night time, then there is almost no point in going to Hongdae in the first place. Hongdae comes to life at night, not in the afternoon. Suggest to just skip Lotte World all together, nothing special about the observation deck to be very frank with you.

I suggest spending your time in Hongdae instead, lots of things to eat, do, and party. If you want, you can even go to a Nanta show.

Gyeongbokgung is cool and all, but it's the more popular palace and thus it's also the one with the most generalization for foreigners. Changdeokgung on the other hand is a lot more true to itself and the secret garden at this time is just BEAUTIFUL! But since you are going to the Hanok village, I guess Gyeongbokgung is the more logical palace to visit.
As a person who resided and worked in S.Korea for a few years before, yes this is a real thing.
However, it's not as widespread as that article is trying to claim. Just like you've never encountered such thing in Taiwan, can you say that it isn't happening in Taiwan?

The foreigner menu thing, that's given to foreigners because they THINK that you won't be able to eat their spicy food or in some cases - some "ahem" meats like; horse, dog, or whatever in the more extreme cases. Sometimes they are priced differently because well... the ingredients that goes into the "foreigner" menu is different too. If not sure, just ask. If don't know how to ask, then too bad - learn how to ask.

I personally has never, ever (not even once in my 3 years at S.Korea) been given a foreigner menu though, not even in foreigner infested areas like Myeongdong.
As for transport, lol if you take subway how the heck is the subway going to cheat you? If you mean taxi drivers, they always use the meter BUT their meter is counted based on how far the distance from point A to B is.
There are obviously drivers who would take a long route, but at the same time how are they going to earn if the passenger wants to go from say Gyeongbokgung palce to Changdeokgung palace? The route is like 5 minutes tops (with moderate traffic), the petrol used to get there would cost nearly as much. So how? Charge 2000 yen and call it a day?

As for clothes, pandai pandai lah. Who ask to buy at flea markets when you know they were all imported directly from China anyways. Same thing in Malaysia what.
Finally, what makes you think tour agencies aren't scamming their customers either? I look at their itineraries and I know some of the places aren't even tourist worthy, many of them are questionable. But let ignorance be bliss right?

Your "simple question" was "I heard my friend said... blah blah blah" then I read this link "saying blah blah blah".

No, you didn't talk about buying clothes but you gave an example so I was clarifying that example:
As for the tour thing, I was clarifying the "Advised its better to take tour" sentence. But no, you didn't claim anything about tour agencies not scamming others. I said that to make a point to compare it back to you where the "advice" to take tour over free and easy is a better option.

And finally the taxi fare, I'm not justifying them. I'm simply giving you a POV form their perspective. Just like in KL, there are almost an equal amount of shitty taxi drivers in Seoul. Does that make you feel better then if I said that instead?

I didn't put a single word in your mouth, you took my words and think it's already in your mouth.

Did I sound like I had prejudice against you? I was straight forward to the point and if that's offensive, then I'm sorry you feel that way.
I meant no offense and yeah, take it how you will then.