First of all, current setup
-wired apple tv 4k gen2 as main apple hub and thread border router
-3 total apple homepods and homepod minis
-ha skyconnect
-ikea dirigera hub
Those make up my primary thread network. I also have 3 aqara devices (hub, thermostat, doorbell) on a separate network. Can't tell if allowing them to join would help or hurt.
Lastly I just recently added the dirigera and intended to not include it as part of the main network, but it joined automatically. I'm fine resetting its thread network to form its own if that is determined to be the problem. I'd prefer not to use it at all but I already had it lying around and my opinion is the new ikea stuff gets more functionality using it (at least until they expose binding on their stuff!).
Now that that's out of the way...
I frequently have issues where a routing device will drop offline and, depending on how it was being used in the network, take a block of devices down with it.
I frequently experience an issue where Apple Home can see devices are online, recognize if a state has changed, but cannot be used to change the state of any of them. Meaning if I turn a light off using HA, Apple will update to show it as off. But if I try to turn the same light off using HK, the icon spins for a bit, the device briefly switches to showing offline, then the state in HK goes back to showing what it was before. Nothing ever happens on the device itself. To combat this, I have removed many of the Matter-connected devices from HK and then exposed them back through HA. HA is never unable to control them (unless of course they are offline due to issue 1). But this does sort of defeat the purpose of Matter imo. And just for clarity, this is specific to MOT stuff. No wifi devices have issues.