Perthaps you could outline how usual submission process goes?

1. Either dev submits their game thru GOG submission process or GOG contacts develeper that is developing promissing game.
2. GOG staff evaluates the game and contacts the dev within two business weeks on average.
3. If GOG is interested and was given sufficient details about the game, dev and GOG negotiate the distribution deal.
4. If agreement is reached, GOG and dev prepare the required marketing material for GOG release.
5. Game is released on GOG.

Anything to add, correct or clarify?

When or what state should dev submit their game? Prototype, alpha, beta? As early as possible or near release?
Because all games published on GOG are featured on front page and gets publicity campaing on sosial media, how long does all it take to set up before actual release?
How long before release day, on average, should submit ready for release version of their game?

As devs seem to think GOG's approval process is obscure, perhaps more info on submission page is in order or perhaps GOG needs to be clearer in their response to devs to avoid confusion?

Oh and you still have the "One World - One Price" slogan on your submission page btw.

Steam had similar problems before greenlight as indie devs felt it was extremely difficult to get on board unless you had publisher backing or already had published game on Steam. They complained that the approval process was obscure and Steam seemed to approve and reject games without rhyme or reason. Greenlight was, for all it's flaws, developed precisely to fix this problem. It, combined with early access, encourages indies to submit their games as soon as possible in order to clear greenlight process and enter early access as early in development as possible (some don't even have much of anything to show, other than screenshots and prototype gameplay videos, before they already get approved thru greenlight voting). While it too is unpredictable, I can see why indies prefer greenlight over negotiations with corporate suits and lawyers.

Edit: One last thing. Was Xenonauts' submission flat out refusal or misunderstanding (I believe this was early 2012 or so, not long after you opened GOG for indies). And would you still refuse an indie or Xenonauts specifically (as was stated as reason at the time) for demanded high price (25$) considering GOG has already approved and sold indies with higher price tag? I'm just wondering if there was a change that Xenonauts would be approved should they redo their submission now considering that they are near release now unlike back in 2012. (Funny that originally the game was supposed to be released by the end of 2012. It's already year and half overdue.). You can aswer hypotetically to later part if you can't answer or can't find details about earlier submission.