...to have a neutral comsat in the natural/other expos?
-Depends on how the map hurts T to balance it. Been done before.
...to have neutral machine shops in the main?
See above. Been done before.
...to have 30 damaged power generators blocking the rushing path that burn down by themselves a few minutes into the game?
Your distances would have to be flawless, and I mean Testbug flawless. Which they aren't.
...to have neutral creep covering the natural?
Depends on other options such as a backdoor expo or close 3rd.
...to have "suggested" sunken placements dictated by neutral creep, like on Colosseum?
Maps have done it already, its obviously do-able.
...to add "gas only" expos to maps?
Eh, not really a good idea. Hurts just about everyone except Z I think. Again, would have to hurt Z in another aspect.
...to have permanent dark swarm(s) covering the mineral lines of bases?
Depends on which bases and the overall design of the map.
...to d-web ramps?
Been done. Balance-able.
...to have neutral spider mines blocking expo placement?
Been done so that only Z can expand early on an island map. DTs have been used to. See Mirage II on BWMN.
...to cover the 3rd gas with a protoss temple?
Been done.
...to place a set of neutral covert ops and silo in the middle of the map?
Impractical. That might work in a game like Red Alert 2 but SC just doesn't play that way.
...to force 4-peon gas in all bases?
That's just annoying.
...to block ramps with a neutral power generator?
Which ramps?
...to make the cliffs in mains unbuildable for 2-3 matrices?
Been done, depends on how you balance the map.