Why don’t you like flatpaks? I’ve basically never had any issues with them, but maybe I will in the future.

As for distrobox, what’s the confusion? Were you trying to do something advanced? Or, was there an issue with mapping things between the host and distrobox? I haven’t really pushed the envelope, but the only issue I’ve had is that I wanted my shell history to be different between the distrobox and the host, so I had to tweak my zsh startup files to detect if I was in a distrobox and save history in a different place.