OK, all of the above problems are now fixed, but we're not 100% there yet.
The fort was relentless in not wanting to export properly, and trying to find whatever unreasonable and mysterious problem the geometry had was hopeless.
Instead, I circumvented the problem by creating a simplified, invisible mesh to act as the fort's collision detection, and had the real thing superimposed over it with a locator.
Thankfully, this actually worked! Hits are registered properly and the fort looks good. The irony is that making a collision mesh like this is the modern way of doing things.
Take that, crappy ten-year-old GM exporter!
One remaining issue is that the fort's flag doesn't want to show up. The locators ARE present in the right place, and the fort does fire back, so I must have missed some code somewhere.
The player's ship also spawns facing the wrong way when leaving the port, despite TOOL suggesting that the reload locator is in fact facing away from the port.
I'm wondering whether that's a code error as well...
Anyway, everything is available in this package:
QC_NEW.7z
You also need to copy Blank.tga.tx from RESOURCE\Textures\Ships to RESOURCE\Textures, so the fort collision mesh is hidden.