Yes, you should be able to use the internal and external connections simultaneously. I don't recall any termination challenges with the 2091, just make sure the Zip drive is terminated.
You should be able to install an RDB to a Zip disk and use it like any other hard drive. I say "should" because Zip disks have some extra hardware features that are software controlled, hence the program IOTools included in OS3.9 (and 3.5?). Not sure if there might be issues if you don't have that program available. Worth trying, though.
It was SyQuest drives that were popular amongst Amigans back in the day, which I know with certainty could be partitioned and formatted without issues (apart from the high defect rate of the cartridges).
