Using Proxmox with lxc containers, there is no second kernel. It uses the host kernel’s native cgroups and namespaces for process isolation. You can actually achieve the same with just systems and namespaces.
Having said that, I think if you prefer traditional distro packaging, you should absolutely stick to that.
I'm aware of the tradeoffs here. For home assistant specifically, there's two options if you want to stay on the path of first-class support. Run it bare metal or in a VM.
Going a different path isn't a bad choice, or even a big downgrade.
I had fun with all the different ways of running home assistant 6+ years ago, and then decided to embrace a solution that required the least fuss and would hold up long term. I'm happy with my choice, and it gave me exactly what I was expecting.
It's still running a second kernel and entire userspace stack. In my world that's not "very little overhead".