By ordering all the graphical apps After=graphical-session.target and
explicitly calling systemctl stop graphical-session.target from sway,
sway succesfully waits for all graphical apps to have terminated. Note
that for terminals (maybe some other apps as well) the result may not be
what you expect: Since the terminal emulator itself (or maybe the shell,
not sure here) does not wait for its children to finish, programs
launched from the terminal will be apruptly killed in any case.
However, launch a signal-ignoring app from wofi and you'll see that your
desktop hangs for precisely 1m30s on logout! Well, if you have a lot of
programs than hang on exit, maybe decrease the systemd stop timeout ;)