the thing to understand though is that when that email is sent it is after "pricing" department who look at all the rules do the verdict and sometimes you do need to push back and get the change. I recently was told Jordan was not in Middle East because the rule said "Middle East (including Egypt, Libya, Sudan)" and only after a long time on hold they agreed that even if Jordan is listed as Asia in AA classification it is indeed Middle East for ow RTW ticketing.
I agree that Asia allows TWO intercontinental departures and arrivals, so that should not be an issue. Perhaps it is the requirement to travel in a continuous direction between TC1-TC2-TC3? It seems once you start in TC3, you are doing TC3-TC1-TC2-TC3. In my current itinerary DONE4 I have something similar TC2 (M East)-TC3 (Asia)-TC1(N America)-TC1 (S America)- TC2 (M East). When I had stopovers in Europe/M East on the return it was messing up the pricing and they were coming up with a lot of problems such as Jordan not being in M East, so in the end I just booked the route without stopovers with the hope changing the dates/time later if need be....