It was one object, so I assume it would need to be physically merged but maybe not. Eitehr way it's probably bad to have objects crashing through one-another.
Not quite.
As Water says - PCS2 and FS can handle intersections just fine, but you must be careful in how you use them. This is because if you build a ship shape out of loads of much simpler parts that all intersect, then you also get:
1) Massive waste of texture space if you have geometry inside other geometry,
2) A much more difficult mesh to work with in the modelling app,
3) A much harder job bug hunting when much more frequent errors occur,
4) Very tricky UVing processes,
5) Depending on the model, a far more tedious debris and LODding process.
I have found that the best approach is to build the core hull as one object, then detail it up with greebles that are a part of the same object but NOT connected to the actual hull. This makes the mesh easy to work with during modelling and texturing, has no wasted texture space, and also makes it easy later on if you want to make the greebles use detail boxes etc.
PCS2 is also quite happy to convert a bunch of mesh items from one TS group, into a single object. So you do have some choice in how you use it.
Hmm, it can yes - but I've seen doing just that destabilise a mesh for no apparent reason, so it's generally better to avoid it.
It is handy for making glass canopies though - since you can easily ensure the polygons of the glass come last on the list.
