I use a nightly version of Thunderbird. Which means I have to use my own Desktop file if I want it to work properly (and not mess up everything).
It currently looks like this:
[Desktop Entry] Version=1.0 Name=Thunderbird Daily GenericName=Mail Client Comment=Mails, Calendars and Chat TryExec=thunderbird Exec=thunderbird --class=Daily %U Icon=thunderbird Type=Application Categories=GNOME;GTK;Network;Email; Keywords=GPG;PGP;XMPP;Jabber;Task;Todo;IMAP;POP;SMTP;Newsgroup;E-Mail;Mail; MimeType=text/plain;text/eml;text/calendar;application/rss+xml;x-scheme-handler/mailto;x-scheme-handler/irc;x-scheme-handler/xmpp;x-scheme-handler/webcal;message/rfc822;x-scheme-handler/news;x-scheme-handler/snews;x-scheme-handler/nntp;x-scheme-handler/feed; StartupNotify=true StartupWMClass=Daily Terminal=false X-GNOME-UsesNotifications=true X-MultipleArgs=false
It used to have a lot more categories and I also tried just specifying
x-scheme-handler/mailto like pantheon mail does, to no avail.
The desktop file is in my .local/share/applications folder, where I have other desktop files. I can select Thunderbird Daily as my default Calendar application. Or even text editor, should maybe remove that text/plain...
Further, desktop-file-validate has no issues with it.
Yet I can not select Thunderbird Daily as my default mail application, only pantheon mail is available.
I'm on 0.4.1 Loki with the settings app at version 2.3.0