Looks like we have a bug there. Removing the $rotate prop from the antenna allows me to fly through it again, so presumably ship-to-ship collisions vs rotating submodels aren't getting correctly ignored. As a workaround, you could add the $no_collisions prop to the antenna as well, since that seems to work.
As for why it still can't (even partially) fly through the Ganymede, I couldn't say. In any case, if you want some class of ship to always be uncollideable, you should probably use the "no collide" ship flag rather than a modified model with added submodel flags. Although if
this bug also affects ship flags, you might need to use a copy of the original model anyway.