Normally, I use MinTrayR and keep Thunderbird icon hidden ("Only show notifications"), so that a new mail causes another icon to appear ("envelope").
When using FireTray instead, it transforms the default icon, so the icon showing new mails remains hidden.
Right: as explained in the README, mail.biff.show_tray_icon is unset during the session by FireTray. This is because FireTray intends to replace the default biff icon.
Now, can your request be rephrased as: having the icon shown only for new/unread messages ?
Duplicate of #137 #150 ?
It's similar to #137, yes. In Windows + MinTrayR, ThunderBird has 2 Icons:
Can you try 59320d5 ? xpi here
Well, I'll just close this one as a duplicate and follow up in #137.