After reading your solution I made a minor change to mine. In the recovery partition, I moved TotalFinder.osax back to /Library/ScriptingAdditions and symlinked it to /System/Library/ScriptingAdditions:
mv /Volumes/<DiskName>/System/Library/ScriptingAdditions/TotalFinder.osax /Volumes/<DiskName>/Library/ScriptingAdditions/
ln -s /Volumes/<DiskName>/Library/ScriptingAdditions/TotalFinder.osax /Volumes/<SystemName>/System/Library/ScriptingAdditions/
TF continues to work normally. TF should also be able to update without issue as long as the filename 'TotalFinder.osax' does not change. If an Apple update removes the symlink from /System/Library/ScriptingAdditions, it's trivial to just re-link it.