Yes, with an emphasis on generally, because as you've pointed out yourself, sometimes plug-in delay isn't compensated as expected, especially with more advanced bus/aux/sidechain routings, so you end up with signals that can be out of sync.
Also because with different Logic updates, they have tried to resolve these issues in different ways, that means that sometimes, taking a project started in an older version of Logic and opening it in a newer version can produce unexpected results.
However as far as bouncing your mix, what you bounce will be what you're hearing when you press Play and listen to the playback in real time, so if it sounds good during playback, there's nothing to worry about. Still always a good idea to give a last listen to your resulting bounced file before sending it off to make 100% sure everything sounds as it should.