I don't use Thunderbird, but at last check it wasn't accepting attachments passed on the
mailto: URI, so whether it's set to your default mail app or not won't make much difference. The latest release
does support, however, passing attachments on the command line:
/Applications/Thunderbird.app/Contents/MacOS/thunderbird-bin -compose attachment='/path/to/attachment'
But I can't see how to make this useful without having to quit and re-start the app each time your script runs. This was discussed with more detail
in a recent thread.