I am not talking about IR remote control, but HDMI-CEC control. I tried this now and the Apple TV can learn the remote, but there is a mild annoyance that the TV is showing a warning on every keypress covering half of the screen, that this keypress is not supported on the current mode. It looks like that both the tv and the Apple TV is trying to interpret the IR codes. Also I cannot teach the playback controls because I dont have all the rew/fwd, prev/next track beginning/end buttons on the remote, only play pause stop rew/fwd.
Maybe switch aw in the watch.app on the phone?