Before any mods,are you certain the Xantrex regulator
Will the warranty remain valid if the Yanmar dealer makes the mod? If not, take it up a level and ask a Yanmar factory rep if this would indeed void the warranty.
if you haven't yet installed the alternator, maybe now's the time to return it and consider a Balmar
or similar alternator, already set up for external regulation.
Or... wait out some or all of the warranty, then do the mod.