Nuke: probably. It'd require hardcoding a lot of it, but something like that could be toggled using a ship flag.
I think, though Bobb would probably know, that in order to really have hud gauges on a ship's textures we'd need to go to DirectX 9, which has a special RenderToTexture function.
Anyway, my guess on the clipping stuff then is that the clipping plane isn't being computed with enough accuracy close-up to render the polygons close-up. There was a similar problem in T2 if you got far away from water.
If I'm right, though, it'd probably involve some VERY low-level modifications to the rendering engine core.
Edit: Oh, and this might sound a little conceited

but in-game cockpits do add to the feeling of the game. Flying Bobb's Hercules and being able to see the gun ports to the sides and look back and see the engines was pretty cool. Even Mechwarrior 2 had that, and it used a purely-software renderer built from scratch. (It was pre-Win95)