Okay, the lil half-saucer shape under the cupula, I can't get it to weld with the other parts. So it seems MOI is not satisfied that the edges line up enough to join it with anything else.

There is a half-circle shape on the underside as well, and it refuses to join with pieces as well.

Deleting them, and performing a blend, the resulting shape works fine, and I can join the starship back up again.