You really painted yourself in a corner with the QNAP setup unfortunately. There’s no way to migrate over to NFS without headache. Moreover, if you want to go the Docker on Linux route, you’re headed for the same headache but different. You can’t really treat iSCSI/LUN as a run of the mill filesystem (as you’ve discovered).
The issue I see is you’re virtualizing everything. Docker was essentially built to negate the OS. iSCSI virtualizes the filesystem. Doesn’t quite matter what you end up running them on really, you’re a slave to each in a sense.
I’ve always favoured running on the rails with this type of thing to maximize compatibility and limit overhead and headache when it comes to potential migration and connectivity to your NAS. Ubuntu server on ZFS running SMB gives you the broadest compatibility and today probably the best performance even on Linux. Moving to NFS doesn’t seem worth at all imo, it’s just a lateral move with a costly bill at the end.