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What I like about running a hypervisor and true vms is that I can fool around with some vms in my server without risk of disrupting the others.

I run most of my dockers in one VM, my game servers in another and the Jellyfin instance on a third. That allows me to fool around with my portainer instance or game servers without disrupting Jellyfin and so on.
Part of it is that I'm more used to and comfortable in managing vms and their backup/recovery compared to LXCs and Dockers.
Im running a similar setup (ZFS pool, Cockpit, portainer x2, and a few LXCs for Plex, Frigate, etc) and it's been great. Before building it early this year, I'd been running everything on Windows for the decade prior because I was unfamiliar with Linux and struggled like OP when problems arose, but after following a guide to get everything setup it's been rock solid and if I screw anything up I can just load a backup. I'd also looked into TrueNAS and Unraid but this gives me a more flexible setup without any extra cost and the ability to tinker without affecting anything else like you said.