Just as a data point, I am running the latest TestFlight (11.6.2052) on two AppleTV 4K’s, and am not experiencing this issue as you’ve described it.
One AppleTV is controlled by a Harmony 650 (infrared only) and the other is controlled by a Harmony Companion (set up as a Bluetooth keyboard.) I am able to manually enter channel commands with both of them, as I have been able to since the start, and it works to change the channel I am watching in Channels.
I haven’t changed any of the configuration, haven’t removed or re-added any part of it, and it all still works.
I have never been able to manually enter channel numbers when in the guide, though. I tried it a long time ago, and it didn’t work then, and I didn’t know that it had ever started working, so I’ve never missed it. I’ve only changed channels this way whilst watching live TV.
That said, I did read elsewhere that there is a newer entry for AppleTVs in Harmony’s database, called “Harmony Pro BT Apple TV 5.” And with this newer entry, there are now true REW and FF buttons. (No more press and hold to get REW and FF. The left and right direction buttons still work as before, so pressing them will skip back and forward, respectively.)
I’m still using the older entry, and it works fine for my needs, so I won’t be changing anything soon. But I mention it in case that newer entry, or some other one, is what’s caused your issue.
What specific settings did you choose when configuring the Harmony to control the AppleTV?