I discovered some errant behavior related to what moving part in the entire FreeSpace machine, that there is fortunately a relatively easy workaround for. If you select the FreeSpace 2 campaign in FreeSpace 2, close the game, and attempt to open a mod that uses FS1 era ships or simply does not use FS2 ships, you'll get a crash error, the usual "Cannot load GTF Myrmidon" like it's attempting to load FS2 ships. I suppose this is partly due to the fact that there's likely no way to force a mod load to change what the player's currently selected campaign is, and trying to open FSPort MVPs has a similar issue.
Fortunately, I found I could launch the base FSPort (no MVPs), load into it, go to the Campaign Room, and choose FreeSpace: The Great War, and then close the game. After that, I seem to be able to load into other mods without trouble.