I have a
single remote to control all components. I solve the problem you share by using remote modes. Even the cheapest universal remotes under $10 typically have a few modes, usually called TV, Aux, Cbl, Sat, DVD, and similar. 3 mode example from a cheapie remote…
Click into TV mode to control only the TV (menus), click into Aux or Strm to control only AppleTV, click into another for any other device.
Typically, the TVs own remote has a few mode buttons, as will a Receiver remote (mine has about 12 modes) and even a Cable or Satt or DVR remote to overcome exactly those kinds of issues. Modes generally “just work” too. Here's a typical Receiver remote's MANY modes...
...coinciding with the many inputs on a Receiver. Put it in BD/DVD mode and the rest of the buttons on the remote will control a disc player (only). Put it in CBL/SAT mode and the rest of the buttons control the CBL/SAT box (only). And so on.
Modes use
unique IR for all of the buttons, so the TV “eye” vs. the AppleTV “eye” watching for IR commands never act on the
same command at the same time. Why? Because up (button) or menu or play button in TV mode sends a
different IR signal than the same button presses in AppleTV mode and DVD mode and Aux mode, etc.
Since AppleTV can learn
any IR remote, if a person doesn't change the mode for that learning, they will be teaching AppleTV to watch for the very same commands used by something else... like the TV (if in TV mode). In that case, BOTH TV and AppleTV will be "seeing" IR commands and taking action at the same time. TV & AppleTV are not smart enough to know which one user intends to react to button presses, so they both simply do what they are "told." The fix for anyone in this situation: click a different mode button and have AppleTV re-learn the same buttons in the other mode. Then TV will react to button presses in TV mode and AppleTV will react to buttons pressed in AppleTV mode- BOTH operating
independently of the other... much like have a bluetooth keyboard with 3 mode buttons so you can put it in Mac, iPad and PC modes to use it with 3 different computing devices.