Set Thunderbird as default app

In that case you could file the issue, maybe against GNOME Control Center. You might be redirected to another component, though.

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I guess Junction could have been the issue?

What exact step solved your issue?

add the following to ~/.config/mimeapps.list:

[Default Applications]
x-scheme-handler/mailto=org.mozilla.Thunderbird.desktop
text/calendar=org.mozilla.Thunderbird.desktop

[Added Associations]
x-scheme-handler/mailto=org.mozilla.Thunderbird.desktop;
text/calendar=org.mozilla.Thunderbird.desktop;