Wait a minute. If Unity has this problem, then this means that the hack's approach needs to be amended. As it is at the moment, one cannot use the hack to reliably get the correct order. This should have been tested before hand.
In my case, how do you propose to get the exact order of the objects after the user has dragged the objects around. What sorting order would you use. What hackery should I employ here.
Edit: If you don't mind, I would also prefer to get the solution to this problem via a unity package. You've requested for me to send repos of the problems. This seems to be an effective and quickest way to find the problem. Likewise, instead of a a million questions of the how the solution should be, please reciprocate with a solution repos. You can post a dropbox link to the file so anyone needing the solution could also get the answer.