This isn't like the A3 no-noise pipe debate. The pressure exerted upon a closed system of brake fluid needs to be able to move the brake caliper pistons. If you increase their size, you have to increase the pressure required to move them. If you don't do it by upgrading the master cylinder, then you must do it by moving that master cylinder piston further. I don't know about your car, but I think your pedal bottoms out the same place mine does. So, if you can't increase pressure with more leverage and you don't allow yourself a means of increasing it through swept volume, the net effect is lower pressure at the brake caliper. And that means poorer brakes... even if they are "bigger."
Well I didn't bring an EA pipe up in my comments so...
The thing you are ignoring about saying lower pressure equaling less braking force is that you are applying that lower pressure (which is arguable too) over a greater surface voulume. You have increased not only rotor clamping surface area, but also piston clamping area. Lower pressure over a an increased volume will exert a similar force. If it did not, then your braking distance would increase with stopping efforts, not remain the same. As typically happens with a BBK. Let's avoid that "my car stops better with a BBK" argument as in general this doesn't hold true either. You are doing a BBK for fade resistence, not stopping distance improvement.
What your argument also misses is the simple real world results of people who run BBK's on their BMW, Audi, VW, MINI, etc. They do not, in general, experience increased stopping distance, as would occur with lower clamping force (the sum of pressure and surface area), almost universally there is no significant change in braking performance as measured in stopping distance. Or at most a negligible decrease in distance, but improved fade resistence and improved track/repetative application performance.