When trying to setup MirrorSync 3 on a 2 machine deployment with separate internal and external addresses, I get an error saying that "XXXXXX.coe.drexel.edu is not a valid address for MirrorSync Internal Address" (and this same thing happens for the Publishing Engine and the Database Server, but only the internal addresses).

If I change the addresses to IP addresses instead I can get to the next screen but when I try to copy scripts I get an error saying that there is no MirrorSync layout on the server even though there definitely is.

The best thing that I can think of is that this has to do with an SSL problem since the SSL certs that are installed on the server were created based on the external address and not the internal address. Does this make sense?

Yes, that does make sense. If you need to enable SSL between MirrorSync and FileMaker Server (which in my opinion is not necessary if they are sitting on the same LAN), then you should probably only enable the external IP addresses, if those are resolvable from within the network.

If you were to disable SSL for the hub, then I'm guessing the internal / external IP address configuration would work. You can still separately enable SSL for the spoke, so that communication between syncing clients  and MirrorSync is encrypted.