XEP-0045 does not handle the case of two user sessions joining the same room with the same nick, that was added by ejabberd. And it was implemented in a way that respects XEP-0045, and doesn't break existing clients.

You propose that when one of those sessions exit the room, ejabberd should send https://xmpp.org/extensions/xep-0045.html#example-82

Have you considered that this would confuse the other room participants clients? Such clients implement XEP-0045, are not aware that there may be several sessions with different resources... and will consider that the exit-stanza you propose means the user has left the room completely.

Is there a way as a participant to get presence stanzas for all resource leaving the MUC room to be able to track which JIDs are online with which resources?

No, I didn't find any method.