I wouldn't be so sure about that. If you go through BKK you will be stamped in and out by Suvarnabhumi Airport" immigration. However, and DMK the stamp will clearly say "Bangkok Airport".
You're correct, the VFS website is close to useless. Eventually you will work out that it is really only slightly useful for tourist visas. I used it twice for that purpose last year and everything was fine. But I wouldn't do the same again.
Curiously it was there in the app some months ago, you had to swipe left on the cards page - "pay like a local" it said. It never worked as far as I know and it's been gone for some time.