It's the sound that matters. There are so many variables in a pickup: magnet, coil shape, coil offset, wire gauge, wire insulation, DC resistance etc. Just one example: Cold Sweat bridge has a large ceramic magnet and is wound with 43 gauge plain enamel wire, DC resistance is around 14K if I remember correctly. Cold Sweat neck has Alnico V magnet, thinner wire than the bridge model and it's around 17-18K (don't know exactly). ;) In case of a Mule set, though, where most components are the same, the neck model will simply have lower DC resistance (don't know if the coil offset is the same in the two models, though).
A calibrated set means that you can set both pickup heights for the best sound and they will still sound perfectly balanced together - no need to compromise tone to have a balanced set. The middle position will be finally useable as well.