As has been intimated in another thread flying (via the flamethrower or alien weapon) in the low gravity environment of the Pfhor ship hasn't been implemented yet. In the original game you can use either weapon to access the secret area without using the lift. But why you would want to do this I don't know since the lift is quite convenient. However there are other high areas you can access, including getting back to the start the quick way. Aside from this it's just cool to fly over your enemies as they gaze in stunned disbelief at the tool of their destruction. ;)
The motion detector works (or doesn't) just like the original. Durandal explains why when you get back to the Marathon:
Your trip to the Pfhor ship was a success. I have learned
valuable information. You may have noticed that the Pfhor
ship has a weak artificial gravity field. The resultant
gravity is lower than the Marathon's. The Pfhor gravity
generators also create a pulsating magnetic field which
interferes with your motion sensor by making it less accurate.
Killing an Enforcer with the rocket launcher won't destroy his alien weapon but the flamethrower does, as per the original game.
Activations all appear to be correct and traps are sprung pretty much the same way as in the original.
Sounds are all implemented correctly and Pfhor goo causes damage when you simply pass over it (something the original M1A1 didn't do).