I have run HA in a python virtual environment as well as hassio running on a Pi3b. Hassio is easier to setup and also to maintain. I made the transition when Homeassistant required new versions of Python.
It works very well for my enviornment which is a combination of z-wave and network attached devices.
I use home assistant in docker. I donāt have to deal with any python versions or hassio issues (see the ingress post where there were lots of bugs dealing with accessing ingress points)
Straight Docker is just as easy for me to manage as hassio on docker and thereās not another layer on top of my HA instance (supervisor)
That was the devs trying to sneak in Ingress without proper communication with devs or users. It was in 0.91 but nowhere in the release notes.It was announced after the third patch made it function.