There is an input brake line on the side of the linked left front master cylinder and an output line on the top. I think the fluid is circulated through the cylinder during the rear caliper outter nipple bleeding procedure, while the piston is in the relaxed state. When front wheel brake motion activates the piston, it closes the input port to apply pressure to the rear caliper, just as the front handlebar master cylinder piston closes it's reservoir port to apply pressure to the front calipers.
Sorry if I sound stupid, but are you saying that the piston I'm looking at has two lines? One on the side (I seem to not be seeing) and one on top? I see one on the side (facing the fork) but that bolt has two lines...one going up and one going down to the caliper. Is that the one you're talking about? Side (front) feeds in and top feeds out? How do you bleed that piston or is it more of a pass-through line so bleeding the rear automatically flushes air out a rear nipple once it runs the whole loop?