Re: you'd 'nohup' them to keep them running when you logged out
I think this is exactly the point. While it's not immediately desired behaviour, it's eminently sensible behaviour and should be expected if you're trying to run processes as an unprivileged user. After all, most systemd processes when started from unit files are daemonised, even those run as unprivileged users. And that's the way the (terrible) systemd manual says they should be run. I'm going to guess the problem is somewhere in the middle of Polkitd and systemd.
I can see there's a need for it, and I'm a Debian user, but personally if I have background processes to run that I need to stay running I make sure they're going to carry on running after I log out. That's probably why I haven't encountered it.
I'm on the fence as to whether or not this needs to be fixed or the requirement for a persistent process needs to be specified in some other way. Otherwise users could be left with a bunch of processes running simply because they didn't explicitly stop everything in logout.