I seriously doubt anyone at SD will come by to help, but I'm bumping in case someone can help.
I know how to make new starbases for added modules, but I don't really know what ILO is or jumpgates are, and that could be why nobody's been sure what to say until now.
No idea how adding starbase modules to factiondefs would work, doesn't sound useful at all, but you can set your own models for starbases and their increments of upgrade in shipstyles.xml