with FSO it would probably work althought intersections, you just can't be sure of the result until you try it in game: Bobbau's enhancements of z-buffer code made the engine more flexible in those situations.
Btw remember it is ALWAYS better to avoid intersections and make solid objects
about pcount..IIRC with FSO you can have around 3000 polys x subobject ( limits have been already bumped in actual FSO), but until the HT&L system will be released, it is better in my opinion to don't go over around 1500 polys for a fighter.
You can reduce a lot the pcount, consider that you vasted a lot of polys in many points.
With a wise use of the shadings, you don't need overdetailed circular shapes; for example, on a shape so small like a fighter, a cylinder of around 12-16 edges will always look like perfectly smoothed, therefore you can reduce a lot the pcount without loosing much quality