Edgecrusher, you are right on the verge of why pressure isn't just pressure.
In Thermodynamics and Fluid Dynamics, we learned that pressure changes when the flow changes like in an elbow, or due to constriction or expansion of the boundary. Also, the fluid changes temperature in response to changes in flow, and this also changes pressures. We modeled flow systems and could see turbulence, and even flow reversals, in response to changes in direction, volume, rate of flow, etc.
So interesting things happen in a 2-line at the 2-hole banjo bolt, and its different from what happens at the junction block, and the flow of the cross-over hose, used in the 3-hose arrangement (OEM).
The cross-over hose is actually going to provide slightly lower pressure to the left caliper as the right caliper is activated, and increases the volume of the fluid boundary, but the system equalizes so fast it doesn't matter.
Its not enough to matter on the street, or even on the track.
I think you are right, MotoGP and WSB bikes and newer exotics all use 2-line configurations for simplicity and ease of maintenance more than anything else.
Living the Gypsy Life