I am still very much liking the dual brake levers, but hate to admit I never have installed the rear double banjo bolt; basically the rear brake foot pedal brake line is not connected and is taped up on the piston end. But as far as connecting both master cylinders to the same line, I don't think it would be a problem. If you've rebuilt a master cylinder, you can see that the lever pushes a piston that acts as a one-way valve: the brake fluid can only be pumped out of the top reservoir into the line, but the pressure in the line normally doesn't push fluid back up into the reservoir.
I am still using an economically-priced left master cylinder:
http://www.ebay.com/itm/Left-7-8-Motorcycle-Handlebar-Hydraulic-Brake-Clutch-Lever-Master-Cylinder-New-/322084724157. This has a 14mm piston and that feels good to me as far as lever travel and feel.
I have ridden ~ 5-6k miles with this setup and still really like it. Also, I have had ICE bikes and have swapped bikes often, and I rarely get confused... although when that does happen it is when I first get on the Zero and pull the left lever (as if it were the clutch). There have been a few times when I've been on my gas bikes and pulled the clutch in thinking it was the brake... but since you are shifting with the clutch to even leave your driveway, you automatically remind your left hand to do the right thing. In emergency stops, pulling the clutch in isn't going to hurt braking and is recommended anyways to not kill the engine. And likewise, pulling the left lever in an emergency stop on the Zero ("on mistake", thinking it is the clutch lever) will just add braking power, which is what you wanted anyways... but yeah, I should have the foot pedal connected just in case of a panic situation where I get confused.
In hard braking it is of course tricky to modulate the rear brake from locking, but the feel with the hand lever is much better than with the foot lever, in my experience.