SRMs and LRMs on Mechs are fine, both enemy and friendly. It's only base defenses. On the Subject of Gauss and Autocannon Defenses, I can confirm Gauss does damage, though it appears to be pathetically small (I guess thats part of the balancing, but it seems a tad extreme for me to be able to park a Lao Hu in front of two Gauss turrets for a minute and have them only do a eight of a health bar of damage.) Autocannons also appear to do damage, but it's tiny, so I didn't notice earlier. So it looks like it's exclusively Base missiles, both short and long ranged, that suffer from this problem.
Another thing I noticed, when I just ran the Davion Moonbase mission, after I captured the sensor array I noticed a few enemy Mechs were destroying the walls of their own bases. The base Defenses did not return fire, and after a few walls were down the Mechs moved on, but it echoed something I had seen a few days ago and completely forgot about. When I did the bandit leader mission, I kept hearing about Turrets being taken offline, and once I got to the main enemy base, all of the Turret Power generators and several turrets had been destroyed. I dunno why It slipped my mind, but it appears that in some missions the various enemy units and objects become hostile to each other for some reason.
On a non bug-related note, and purely because I'm OCD, if I were to take the movie files out of my old MC2 install would there be any way whatsoever to get them to play in missions or has the code become completely incompatible?