ADK,
I downloaded your operating manual and I see exactly the situation you're in. It would be nice if the trigger had an "all" selection, but it only has zone 1,2,3,off. Also, if I'm reading your post correctly, when you select MR&S in rear surround mode, it switches the rear surround speaker posts to zone 2, but at the same time, it also switches the RCA rear surround preouts to zone 2.
I can think of only three ways of compensating for this, but none are perfect. It's tough. Maybe somebody else will see this and have much more intelligent comments to add.
Option 1. Run the trigger from zone 1 and always run zone 1 whenever you need zone 2, just keep the zone 1 volume at zero. This is probably what you already do.
Option 2. Since there is not really any 6.1 programming material, use the MR&S surround setting and run zone 2 from the receiver's rear surround speaker post. Split the RCA signal from a surround output with a Y adapter and feed it to both the surround and rear surround channel of the 7.1 amp. This way all 6 zone 1 speakers are run off the main amp and zone two doesn't need to have the amp on at all. But there's devils running all over the details of this as well. It would be easier to set up if you have gain control for each channel on the amp and if you picked up one more RX-4 to split both surround channels to run 7.1.
Option 3. Run the 6.1 from the regular preouts to the amp in zone 1. Get another 2 channel amp and run it from the MR&S outputs. Assign the 7ch amp to zone 1 trigger and the 2ch amp to the zone two trigger.
One caveat also. Check with others before you take any advice from me. As I said earlier in this thread, "Lots of things don't work out for me", but it's not for lack of trying.