Some master cylinders are set up for discs on the front and drums on the back, so in that case I think you need to hook it up in the correct ports. But on ones that are set up for drums, and if you are using drums, I don't think it makes a whole lot of difference. It could be that certain master cylinders have different sized bores too.

On my T I ran the master cylinder facing the opposite direction, and simply hooked up the lines so they ran conveniently, without regard to front or back, and it seems to work fine.

Don