For 1999, Ducati redesigned the electrical system, going from the 350 watt design to a 500 watt three-phase system. (Three-phase alternators have three wires coming out of them, single-phase have two.) They produce an AC output that has a higher frequency than the earlier single-phase design so the regulator presumably has to do less work (i.e. less heat) conditioning the waveform and converting it to DC. The RR51 is a single phase unit, the RR53 is a three phase.
Some people have asked whether you can convert a single phase to a three phase system. Not very easily. You'd need to replace the crankshaft, rotor, stator, alternator side engine cover, clutch slave and pushrod, etc.