First, who are you to say "WARNING, STAY AWAY" when it's a very minor issue and you KNOW that a very, very small percentage of ppl have a similar setup to yours. Now instead of jumping up and saying, makes my replay totally useless, why don't you figure out a solution? If you make duplicate timers, one on the 322 telling it to auto-tune during the program you want, then you wouldn't have a problem.
A bit more work, but you shouldn't be using the Replay with Dish anyway. I mean, it would be a lot easier just using Dish's DVRs, and if not then crawl over to DirecTV for their Tivo.
Another solution, not sure if it's feasible is have your Replay unit transmit something to your 322 every 3 hours that won't affect anything. Like a single button press, or make daily 1 min timers every 3 hours. I'm not sure, but I'm sure you can figure something out to not make your Replay unit totally useless.
Edit: Sorry, didn't read all of your post. Instead of suggesting disable screensaver and such to Dish, how about suggesting that instead of having to press select to disable the screen saver, that you could press any button?