I locked myself out of my site and had to use the "Help, I have been locked out of my site's administrator area!" via plugin/system/admintools/main-disable.php process.
After doing that, I got into the backend to re-eanble and got the big red WARNING message which freaked me out (It was scary enough having locked myself out!).
I understand FULLY the need to stress that there is no support while that message is being displayed, but is it possible to add to the message something like. "If you are getting this message because you have disabled main.php then take a deep breath and sort your issue out as per the trouble shooting documents.
This could possible go after the bit about the Joomla bug.