If you look at the "raw table" of departments, you only see that one associated with your subsidiary. But if you select department on e.g. an item, you see all subsidiaries departments. Can this be fixed?

This appears to be standard behavior (I also see the same thing in my test account). I know that for department/class/location restrictions, there's a specific box to also apply those to items but that doesn't seem to be the case for subsidiary restrictions. You do get an error though, if you try to select an incompatible department/subsidiary combination though.

Yes, we do get an error when I try to create a transaction with general ledger impact.