Does Master cylinder bore size really make a difference.

Your description isn't entirely clear — are you saying you installed a disc/drum master cylinder on a car with drum brakes?

That would not be as bad as using a drum/drum MC with disc brakes. But it still leaves open the possibility of a few odd side effects.

Also, the smaller bore MC should make the pedal seem SOFTER, not harder. So I suspect there was a problem with the original MC, and the improvement is due to fitting a properly working MC rather than the size difference.