So its been a few months.. I've been having my field users regularly log out and log back into Field Maps while on the Network and otherwise just conduct their field work as normal, business as usual. I always have them manually log out / log in in Field Maps prior to removing any Offline Areas.
This seems to have reduced the times where I see the orphaned versions error and I have been able to smoothly pare down the version list and delete Field Maps versions after projects are completed as expected without resorting to the SQL Server route.
So maybe it just needs more frequent log out / log in to Field Maps while connected to the network? I don't know. If we don't perform the log out / log in Data Collection and Sync seems to work just fine.