I don't think the OP is asking if any Harmony/programmable remote can mimic the AppleTV remote. It's IR, I can't imagine it not working!
What the OP asked is can you train the new AppleTV itself to respond to an entirely different set of remote commands. On the original AppleTV, you could go into settings, and "teach" the AppleTV commands from any given IR remote. I trained mine to respond to the second control side of my TiVo remote. It worked great!
I hope they didn't remove this feature, but who knows!