Welcome. Yes, the 12 frame is a funny one. I think they designed it and then thought "hmm, what do we do about a queen excluder on this thing?"
I have one, but I don't have the QEx as I don't use them.
Yes, their excluder is meant to sit directly on the frames
In theory this is OK, as long as you are careful not to crush bees when putting it on (easier said, with a rigid metal QEx)
But I wonder - could you test something? Put the QEx on, and the super box, then put a super frame in. How much space (mm) is there between the bottom of the super frame and the QEx? Enough for a bee (i.e. 6mm or so)? Ta