Sorry been busy and away for awhile. I dont even remember much of what the scripting was like in the old mod about emp since so much of it was rewritten from scratch.
As for the car (and all the others like it), sounds like telefrag checks so players dont get stuck and easy targets. The default is that players are visible, for the duration physically occupying the space, and are thus shootable. Doing it with the invisible setting has some compromises and this is one of them. Just to note, telefrag checks have also been used since the beginning of the game (and thus a built in engine function) to prevent players from spawning on the same spot and being stuck in each other. Assuming the mapper included enough spawn points which sometimes they didnt.
For those that remember, telefragging was a popular method of killing enemies using the translocator. One reason why a lot of places shut it off. Great fun if you were good enough to do it.