To elaborate on why this most likely is:

This is probably due to the wormholes, most likely there was a perimiter placed so that starbased cannot be placed in the centre of a wormhole (thereby blocking passage through it ) and this carried on to other special uncolonisable things, it may not apply to all of them, as you said, but it does prevent you from placing it there.

Isn't near centre close enough? I would place it near where the enemy would phase in, or where they would have to phase out from, but more likely where they are phasing in is a better idea, you get them by surprise; just a tidbit there.

Actually, from what I could tell, it's because when you mouse over the center you are treated as having moused over the grav well itself's info (e. g. as if you'd moused over the planet/asteroid that would 'normally' be there).  And you can't build on top of an existing unit, so...

No, what he's describing is a real error -- go try it yourself!  If you try to build near the center of a grav well, the build icon snaps to the 'center', where you can click to see info on the grav well itself (like abilities).