It now works! I posted the question on the Dish forum and was told "most universal remotes require the IR address to be set to 1." So, I reset the remote address on the box to 1 and now both the 21.1 and the MX-900 work.

Steve_the_Man also told me to try 1 but it didn't sink in. I didn't quite believe it because I had the mindset that I had to make the MX-900 emulate the new Dish remote, and it switches the box to 3 when registered. Hence, I thought 3 was the magic number. Also, I had tried 1 early on when I was trying to make things work in RF mode, but since the TV2 remote (which is RF) already has address 1 that address for the TV1 remote was rejected.

Anyway, the problem's solved. If anyone else wants to use both a Dish IR/UHF remote AND the MX-900 the upshot is:

1. Dish remote must be set to IR (tiny slider switch under battery cover).
2. Register the Dish remote per Dish instructions. This will set the remote address in the DVR box to 3.
3. Go through the instructions in the Dish manuals to set the remote address to 1.