You may need to change either how you model or the modeling package. Only use boolean functions if you are willing to edit/tidy up at the poly/vertex level. Sometimes letting the game engine work out some of the intersections may cause less problems than Truespace's attempt.
Also if you never see a poly in game - then you can delete it. For example the 14 polies under the turret base(x10) etc...
Got your pof in game after re-saving with PCS2, and yes most of the bits had disappeared.
Got the hull in game and then got the skirt in game. Both of these were re uv- mapped (auto with single texture - Blender)
Made a temp table and attacked the ship - most of the turrets were invisible so it was hard to tell which ones were firing.
PCS2 has error checking stuff to catch problems. But all automated fixers are there to catch the occasional error. TS3 does not do booleans very well - and you have done quite a few. For an object that gets copied multiple times like a turret, it pays to get the first one right.
At the end of the day it's FSO that chooses if a pof is usable, not PCS.
( 1k for a gun barrel is high poly
)
So it is fixable with a bit of effort - but I don't think Truespace 3.2 is the App to use. I would recommend Blender (but maybe not to a Truespace user) - possibly try Wings3D. Use it to fix the mesh and then re-import to Truespace.
Nice ship
