Ghostbreed: Give me a second guys!
Update: Okay, for the first time ever, a digital release of Quake finally has the soundtrack included!
As for DOSBox wrapper. I do not know. When I started the game, the 3DFX logo appeared before the game started.
I'm vaguely guessing they use the official GLQuake wrapper then.
Doom uses DOSBox wrapper though. Just checked.
And yes, the SETUP for each Doom game is included.
Sounds like they're using Nglide. It's a 3rd part wrapper that GOG uses for some of their games. It's a good way to get old games working on new hardware with very little getting in the way.