If I am right polkit is now fully dependent from (e)logind and getting it to work with an authentication agent is not an easy job
what do you mean? Obarun Polkit package do not support elogind at compile time.
I think we have two different issue.
First, dbus is compiled without the support of auto-launch a dbus session. That's me that any software which can try to launch a dbus-session will fail. As being said, the dbus-session should be handled by user with the dbus-session@ service. But, apparently some sotware cannot works on proper way and find the dbus session "number".
Second, like jean-michel said more and more software depends on elogind. The consolekit one is not bad or miss features, that's just dev prefer to use libsystemd (and so elogind) instead of making their software portable and compatible. Systemd is not a system manager, not only a service manager.
Complete DE will cause more and more problem due of this fact where WM will keep working correctly. On JWM i don't have any permissions issue.
So what to do?