Is it still possible to separate those out or will it smush all of those into a single export?

Since I've only downloaded the one group, I can't really say.  When I was doing the export it looked as though, if I had more than one database, I could choose to select only one of them.  What I don't know is whether the program would generate (read? differentiate?) multiple databases from one .db3 file if you'd downloaded multiple groups.