I just tried the 2 seperate system files with different zone ids.
It works basicaly the same . If one remote is issueing a volume up for several second and the other remote tries to do anything. The first remote has priority.
If there is no way around this, thats crap.
I just never noticed this on any of my installs because I was just looking for correct communication routing and everything working on an individual basis.
Now that I have it in my home and am using it, I find the problems.
Don't read my answer. Someone else will go into great detail as to why I am wrong rather than answer the original question...