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in order to be work in Todoist, I needed to fully url encode the string (Todoist choked at the @ symbol):

tell application "Mail"
    set theSelection to selection
    set theMessage to first item of theSelection
    set theUrl to "<" & message id of theMessage & ">"
    set theUrl to do shell script "/usr/bin/python -c 'import sys, urllib; print urllib.quote(sys.argv[1])' " & quoted form of theUrl
    set theUrl to "message://" & theUrl
    set the clipboard to theUrl
end tell
  • I saved the script to /Library/Scripts/Mail Scripts as suggested above
  • I installed also FastScript and bound the AppleScript to ⌘L (for Link)

now I can hit cmd-l on any message in Apple Mail and paste the link in todoist and clicking it opens the mail again, thanks internet!