They also separate the games on Steam, I don't think they would create a different version of the game just for GOG, they said on Twitter that the update on Steam make it even with GOG.

You are confused. When I say Battle Chess, I mean the 1st Battle Chess game, not the recently-removed bundle that contained all the 3 games. The 1st game was initially released on floppy disks in 1988. Battle Chess: Enhanced, a CD-ROM version that contained a host of improvements like the addition of a redbook soundtrack, was released a few years later.

GOG only has the floppy version. GOG doesn't have the Enhanced version.

GOG's installation takes up ~15 MBs. Steam's installation takes up ~800 MBs. If Interplay really told you that the versions are equal, then they are lying:
https://steamdb.info/depot/622832/

Superliminal received a free multiplayer update on Steam on November 5th and we didn't get that update on GOG yet.

https://store.steampowered.com/news/app/1049410/view/3105788446475141781

I figured, they even discounted the game on GOG for the update launch, but without releasing the update.

Anyway, we should also add E.Y.E: Divine Cybermancy - Castrated Edition, which lacks PvP multiplayer and Co-op both LAN and online, French language, achievements and god knows what else.

Death's Gambit is missing the Afterlife update (released on 30th September on Steam), which added a whole bunch of new content. It's also missing the soundtrack.

Door Kickers - Action Squad is missing:

Professionals Abroad DLC
Artbook

and also missing the Door Kickers Action Squad Deluxe Edition (base game and all 3 DLC with a 10% discount).

Only the base game is available on GOG.

There are some signs that might indicate that the newest DLC is on it's way here: https://www.gog.com/forum/general/games_that_are_unofficially_confirmed_for_release_in_the_future_part_2/page663#p_b_13277

FICTORUM, I don't have the game but the achievements don't work in gog according to other users here. The developer said it would fix it but lied.

KING OF SEA does not support gog galaxy, developer lied to gog users.

Satellite Reign doesn't work a single achievement. The developers are not going to fix it.

Elex, no gog achievements.

HUNTDOWN no ​​achievements in gog

Banished No achievements in gog

Achievements is not for second citizen treatment nor should it be but there is a another thread to highlight this issue for those interested, one i cannot find right now.

They don't want to include achievs here for some reason, check this thread for the separated spreadsheet:
https://www.gog.com/forum/general/list_of_broken_gog_achievements/page1

This. I think the list should only be for missing in-game content/dlc (including game modding features) and patches. Not achievements or soundtracks/etc that have nothing to do with actual in-game content. Adding games based on non in-game content just bloats the list.

Imagine thinking soundtrack has nothing to do with the game.
This is why we can't have nice things, because you people and your stupid rules of what qualifies as this or that.
Gee whiz, I don't need that cosmetic, it's not crucial. Shucks, I don't need that DLC, it sucks anyways.
You realize you don't have to negate someone else's wishes to fulfill your own, right?
Agree and amplify, or be quiet.

You might refer to this thread. I have to say that I am still surprised that a perfectly subjective opinion could be stated as a fact even though it is not (it only would be if nobody would enjoy achievements which isn't the case) but sure .... anyway, that's not the topic here.

No matter if missing/broken achievements can or should be considered second class treatment this isn't the right thread for it. Alexim is collecting those here:
https://www.gog.com/forum/general/list_of_broken_gog_achievements/page1

Regarding this,

Steam games that treat Steam customers as second class citizens:
- All the games which exist also on the GOG store.
They all lack offline installers, while the GOG versions have them, so clearly the Steam version is lacking a feature available in The Other Store(tm) ie. GOG.com.

Someone might say "But Steam users are not interested in offline installers", but that is only his/her/its subjective opinion, not a fact in any shape or form or color.