The engine really doesn't care... UV overlap is far more about making textures smaller - which it does care about.
Yes, shared UVs complicate AO bakes... though for engines the 'thruster' surfaces are often almost entirely lit by glows, or dark enough that they are 'nearly' black when the thruster isn't on. I feel like it is less of an issue.
Hell, it would be VERY easy enough to make a variant of the ship shader that uses diffuse vertex color (not texture, but one of the RGBA color components) as an AO mult - that way you still get shared UVs, but each one can have a shadow or soft AO in addition.
You could treat the RGBA channels of the vertex color all sorts of ways:
R - Ambient mult
G - Diffuse mult
B - Spec mult
A - A bunch of random ish