Thats a good point, could be some water or moisture in the fuel. As for your maintenance it seems like you're on point. However, with regards to the coolant flush, it is far better to do a complete flush. If you have the funds to take it a tire shop or someplace like that that offers cooling system flushes, I would recommend doing that. The reason for this is that if you just drain whats in the radiator and replace it, you are essentially mixing perfectly good coolant with some that may be depleted (and there are additives and inhibitors in coolant that need to be replenished) and you just dont do yourself or the cooling system any favors by doing that.
With regards to the transmission flush. Its really the same thing. You're pouring in new fluid with worn out fluid. There is a lot of fluid in left in the torque converter if you just do a pan drop and filter change. I have never had any problems flushing transmissions but I respect your concerns. So to that end I would recommend just doing a pan drop and filter change with basic Dexron ATF. Drive that around for a while and make sure everything works properly and once you are happy with that, then do a full flush.
Maybe Trannyman will step in here and give his comments on flushing the tranny, he would be a much more respected source of information than I as he is probably one of if not the top builder of 4T65E's in the nation.