My take is that they're still in Garlean control, but that said control may have changed hands a few times. Remember that Werlyt brings up Caestrum Marinum as now being in VIIth legion control.

The exact nature of the hostile mobs are still kinda time-bubbly, since by nature they still have to remain, but it does explain why people like that would be there and why they haven't been demolished: diplomatically speaking that's still someone else's house. It'd also make some sense for Garlemald to retain it; however they get back on their feet, it's probably going to require trade with outside nations, so the various Caestrums would treat them well as trading posts. Especially since we know they have a train network between some.