AiMesh is the only feature I specifically don't support.
I don't know if Asus recently broke something related to firmware image generation, but this is the second time one of my firmware image has these squashfs errors, and Asus also encountered them with a recent RT-AC68U release. I will have to try digging up what changes might have introduced these.
They should be, but only way to be 100% sure is by testing, since I have no way of knowing what was changed in the closed source parts.
It depends what was in the open sources parts, and what wasn't. Some of these are in the open sourced parts, others aren't.
A user-generated stubby.yml is almsot guaranteed to NOT work after a reboot. Rather than face a number of users struggling with that, I prefer to remove it. Users have no way of knowing that the stubby.yml content needs to be different at boot time than after subsequent restarts.