Update: I can confirm that it is quite safe to transport USORG and USVAR(T) as table entries and then also run SU25 steps in addition to PFCG_ORGFIELD_DELETE and transport that in step 3.
The roles in target systems still have profiles assigned and UST12 does not care about orgfields, but the auths tabs are all red. This means that if you ever entered change mode, it will force the read old / merge new option, which is also correct.
This is OK in my case as the 28 custom orgfields all had a * in them anyway, and the existing roles will soon be replaced by new sets of roles and deleted. We only need to bridge a small time gap where the users don't have the new roles and request something to be done to an old role.
So transporting the definitions through was correct as exporting them in "old status" does not work anyway, and I need to get my new roles live ASAP (which is not a problem - first users are live already).
If you however want to salvage the old roles after demoting orgfields and combining it with a release upgrade, then using this table entries solution to transporting is probably not an ideal approach.
Upgrades are normally a nice opportunity to start over anyway...
I will leave the thread open for a while still if there are other experiences with this or an official process shows up. But my own problem is solved.
Cheers,
Julius