This would work as long as you aren't programming a universal remote that has activities, like the Harmony 1100 that I use. The remote switches inputs for you that resides on the AVR.
I’m not sure what your talking about here. I have my switch programmed into my Harmony activities just fine. It’s own remote is a cheepo keychain size thing but Harmony has all the codes.
On my Denon 2807 I had two inputs one direct for the Oppo and the second with four (DVR, Xbox, HTPC, Gaming PC). All the activities worked just fine and the Denon still remembered the “last used settings” for each activity. Maybe they’ve changed things.