Painting over a scan / sketch can be very in-depth - but in the example that you show, it's rather clear that the buildings retain a lot of pixel details from scanning, with as little re-touching as was necessary.
it make me wonder why people are criticized if they use these methods nowadays to make pixel art.
Mostly the issue of plagiarism (if the source is an artwork) and undeserved praise.
It's not so new, because even 20 years ago there was the "no copy" movement in demoscene, as a reaction to the (over?)use of copying paintings, with and without credit. Boris Vallejo, Luis Royo, and licensed AD&D artists got copied a lot.
Nowadays, galleries like Artcity (artcity.bitfellas.org) and Pixeljoint strongly advise providing sources and references, so that the viewer can make their own opinion.
Making-of videos can be very interesting to watch (or at least skip through), it's not unusual to see that the video is at 33% duration when you'd consider the image finished, but a dedicated pixel artist will keep tuning and fixing and redoing parts that he doesn't like.