Just to clarify, Nathan, you said: I'd LIKE to put holes in the roof...
As in you don't mind making some holes. As when you say bulkhead connectors... I want to understand more of what you mean.
If your intention is to mount an antenna to your roofrack, and run the cable to a surface mounted connector, or bulkhead, there's a couple options, weatherproofing could be an issue for the connection, but not the mounting of the connector.
Or perhaps you mean you want to mount the antenna to the roof by way of an NMO connector, and simply be able to remove/re-install it easily, with or without the rack on top. Also easy, tons of NMO type mounts out there.
A little more clarification, and I think I can help after that.