Hi,
I have to say that your answer is correct. There's no possibility that one SEP client can be a GUP for two separate consoles.
On top of that the SEPM in the version 11.x uses IIS to communicate with the client where in 12.1.x the embedded Apache server is used.
In the scenarion you've described two separate SEPM consoles, running two different versions = 2 separated databases...
And in the end... both of the SEPMs would try to modify the same registry key on the client site to set it as a GUP- they would probably fail
I hope this answers your question.
Regards,
Drl