The intentional and willful breaking of screen and tmux was to fix a GNOME bug of GNOME not closing up as it should when the user logs out, so systemd was changed to mass kill processes. The interplay between GNOME and systemd in backroom dealings is a major pain point.
I think that's an oversimplification. There are definitely cases where some thing started as a daemon under a user session, graphical or not, should be killed to be safe. For example, ssh-agent.
There are other things that are meant to be left around, as that's their purpose, such as screen and tmux.
I would say the safe solution would be to kill everything in the user session at multiple levels (GNOME, and user session management demon like logind, etc), and to provide a defined safe way for the very few programs that want to stick around to do so. That seems like what systemd came up with as well.
