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While it can be true that more pistons can make for longer pedal travel that's not a given. It has to do with volume of pistons. If the 6/4 has more total volume the pedal will travel further, but will have better modulation and higher ultimate force capability. You could make a single piston caliper that was huge and it would have longer pedal travel.

Most brake companies try and match volume as close as possible, and changing it can mess with ABS, balance, etc... I can't image Brembo got that wrong, but who knows.

I strongly suspect they have air trapped in the system (ABS can be tough) and they haven't got it out of the system.