Isn't Quake Engine or it's compiler doing this automaticly (as like merging surfaces together whenever possible)?
Unfortunately no. idTech 4+ does much of this automatically but not id tech 3. I did annoy me for some time because it sounds like a trivial task that the compiler should do for me. Modern engines can do this at runtime.
The compiler will perform one optimization. Surfaces will be auto caulked if they are completly covered by the void. Structural brushes are part of the void. Surfaces only covered by a detail-brush or patch will not be auto caulked.
I cannot work in caulk-mode. I need the textures.