I think both of these ways are good and valid in their own way, they both have upsides and downsides. For me, having things separated is working well. I especially like being able to reboot HAOS more frequently and as soon as it comes back up all my Z-wave devices are ready to go. Back when I ran Z-wave inside of HAOS it took a lot longer for the Z-wave network to calm down and be ready after a reboot.