It doesn't make a difference if you start with a long or a short tunnel, the exhaust support bracket is the same. In fact, the tunnel up to the exhaust support bracket is the same, the mtn differs only in the extension. In fact, this problem occurs with the STOCK mtn, I think 06, and required a number of people to install a ramp over that piece in order to save their tracks and tunnels in the time before Yamaha issued a solution. The track will still rub it, but it won't CATCH.
I myself, with ExpertX-144 (full 144" rails, so it wouldn't qualify so much as "custom"), noticed this clearance problem as well, but I noticed it BEFORE running it. I run a rear heat exchanger, which I modified to sit flush against the tunnel, and I cut down the part of the exhaust bracket that you mention is being caught. In order to prevent rubbing, it also required that the rear mount bolt on the ExpertX be lowered by about 1/2".