If it's worked out, great, but as others here mentioned, playing around with the alignment of the back wheel in the dropouts could have it walking in toward the flange to clear up the issue. Only thing I've noticed with that original system is that it's a fine line between having it sit where you want and having it walk in to the point it rubs the flange, usually picking up a whining or squeaking sound. Best to have or get threaded tension adjusters for the rear.
Also, even though Gates says to run the flange on the inside at the rear, I've known people to run the flanges however they work for the bike they have, when they get into something unorthodox and non-stock. Check the inside of the rear cog and see if the interface with the splined driver is dished one way or the other. I.e., if you flip the cog so that it is flange-out, does that position the cog teeth track further out from the hub?
I know next to nothing. I am frequently wrong.