Actually most of this is pretty well-explained in the manual (no offence meant):
1) "...the bounding boxes of the two entities are tested against each other." Shape: er, box-shaped. Size: see max_x, min_x etc. The box is determined by the size of your model (I think it's taken from the first frame, but I'm not sure.) You can change the size using the min_x, max_x commands...
2) See trace() in the manual. You can set use_box in trace_mode to determine whether it detects the hull or the bounding box. Either way, the trace actually hits the box (bounding box or hull) of the model, and NOT the MDL itself, so if you are emitting blood or suchlike you need to detect the nearest vertex, otherwise the blood may seem to be emitted from nearby the model...
3) The bounding box is determined by the model, so as you can only scale the models before you save them to MDL, this won't have any effect - ie the box will be as big as your model.
4) "The hull is used for collisions of a moving entity against the level or map entities. This (sic) kind of collisions detect each polygon of the target entity." Pretty straightforward...
5) Not sure I understand the question, but seeing as either way the window would be square, it should make no difference - it should be detected just as well whatever type of collision you used.
6) Could be your trigger range. Is the door set to open automatically?
Hope that's of some help, don't mean to be too RTFM on you,
Cheers,
Keith