All ya have to do is the math on which MC is best. The size of the brake cylinders has no bearing on the volume, only on the filling time. If you take a 1-1/8" and put 50 lbs foot pressure on it, you get ~1580 lbs system pressure, take the 1-5/16" and put 50 lbs foot pressure on it and you get ~3200 lbs system pressure. That system pressure is mutiplied by the size of the brake cylinder piston area. If either MC size does the job for the stopping load, thats all that matters.
This kinda concures with what icanfixall found.
With respect, disagree - your math is backwards.
With the 1 1/8 cylinder you have ~1 sq in or piston surface area. 1 5/16 is 1.35 sq in. Assuming the same force is applied, the larger cylinder will produce less pressure - pressure = force times area.
So all things being equal, the larger cylinder with make less pressure with the same force applied....
However, the volume of fluid moved is greater for a given stroke with the large cylinder.
So the larger cylinder, all other things being equal will take a shorter movement of the petal, but more force to produce the same net braking effect.
Now, the caveat to this is that we're considering the booster and the petal to be the same in both cases. However, what we usually do is swap the vacuum booster with 1 1/8 cylinder for the hydro with 1 5/16. The hydro setup given more effective multiplication of the petal force (ie, small force pushing on the petal equals more force on the master cyl piston) due to the more powerful booster and the change in the pin location on the petal.
However, a side effect of moving the pin up on the petal is that the effective stroke of the brake master is reduced. That is, the fixed amount you can press the petal down before hitting the floor equates to a shorter distance the piston moves.
This in turn means that with a smaller cylinder you may have less then the optimal of reserve braking, since you have to move the petal further to move the same amount of fluid.
The short and simple version is that the system is designed as a whole - petal, booster & cylinder. Use all 3 together for the best results because it's all matched design wise.