That's what I thought the purpose was, but the way these Master cyliders are set up, the front port is the one that recieves 60% of the breaking. Right now, mine is plumbed with the front brakes off the front port. When I mash on the brake pedal and step on the gas with the front axle only engaged, ie, rear axle in neutral, the rear tires still turn, don't lock up when the gas is depressed. They should drag as it powers through the front brakes. This is needed to do front digs on tight corners, and since I can't lock up the rear tires, even with the rear driveshaft dissengaged, my front digs are not nearly as effective.
Don't tell me it's a bad MC cause it's brand new, for a 95 to compensate for my rear disks. It did the same thing with the 91 MC. It's the way they are designed to allow more braking pressure to the front. The 91-92 with rear ABS were plumbed this way, the 93-94's with 4 wheel ABS were also plumbed this way (front fort of MC to front brakes) and the 95 and up with 4 wheel disk brakes are plumbed this way as well, so I think that by reversing the ports, you are reversing the brake biasing. The front port is larger to provide more volume as well, which is needed by the larger front brakes. Of course, the only true way to tell would be to put an in line pressure valve on each line to compare the true braking pressures.
My next step is to install a adjustable pressure biasing valve on the front line to allow for a little more rear braking to get the correct ballance. I am also going to put in hand controlled cutting brakes for the rears.