: Did they ever get rid of the M1A1 changes
The version that came with Aleph One 1.0 got rid of all that, yes. Hamish and Bruce Morrison went over each level with a fine-tooth comb to strip out all the additions, fix monster and weapon placements, adjust monster settings to make the battles play out more faithfully, etc.
To make the single-player more authentic, they also removed the other player starts, so you'll spawn on top of each other at the beginning of each level. It looks like most of the network-only ammo and weapons were left in, though.
: Or do the map files do things like put goal polygons in places that you can see but can't get to?
Unfortunately they do. I remember a goal on one of the Pfhor levels being a purely decorative recess near the ceiling. It was easy to spot from anywhere in the room (which had multiple entrances/exits) but impossible to reach.
