I brought this topic to the forum once before when 16.4 first released and made little progress troubleshooting till recently. Since then I’ve been able to reliably recreate the following issue and solution. Hopefully this helps someone who may have run into this same quirk.

Key info: 3 Apple TV 4K, 3 HomePod Mini, Velop AX4200 3 Node Mesh, 28 total outlets/switches/bulbs/air purifier/doorbells, ALL the aforementioned and my phone and laptop are running latest firmware and os.

I prefer Apple TVs wired and pre 16.4 all 3 were wired and one was always the leader.
After 16.4, when a wired Apple TV 4K is the “connected” home hub all thread only devices become unresponsive. I found that disconnecting the Ethernet cable from the Apple TVs and letting them revert to Wi-Fi will ALWAYS allow result in a HomePod Mini taking over as the “connected” hub.
Once the HomePod is the leader, all thread devices perform perfectly. If I plug the Ethernet cable back into one of the TVs, it then takes over and the problem arises again.

So, as long as my Apple TVs are on wifi and I have a HomePod leading, this becomes a non-issue. Despite figuring out this workaround I’d love to hear if anyone else has encountered this and solved it a different way.

Hope this helps someone out there!