Interesting write-up RJB... my opinion is that if the new watch meets (or exceeds) the technical and performance specifications of NASA and of 'the' 1960's era Moonwatch then it certainly can't be disqualified merely on the grounds of not housing a caliber 321 movement (which, let's be honest, is a good movement but is technically inferior to the newer caliber 3861 in the same way that an air cooled engine from a 1967 Porsche 911 is no match for a modern water cooled Porsche 911). I'd certainly prefer to cruise around town in the '67 Porsche, but that's for the nostalgia and not because of any performance attributes.
Maybe a question to ask is, "if NASA was going to fly a crew to the Moon and their lives might depend on having a mechanical watch back-up (ala Apollo 13), would you select a caliber 321 powered watch or one with the new caliber 3861?" If there wasn't going to be any pre-flight testing involved then you might select the 321 simply because it is a known quantity (assuming a new one could be built to the precise specifications), but if NASA fully tested and flight qualified the 3861 I would certainly select it over the 321 due to the accuracy and anti-magnetism performance alone. So both certainly are Speedmaster Professionals, whereas your premise is that the 'Moonwatch' might only exist in time for the 1960's era and can never be resurrected which I'm fine with (at that point, it's really just an argument amongst collectors who won't be wearing the watches as they were intended). A similar question... you're diving in the South Pacific at significant depth and can choose between a caliber 1570 Rolex Sea-Dweller (ref. 1665) or a more modern caliber 3235 Sea-Dweller (ref. 126600) - you and I would probably select the more modern iteration because of it's performance and reliability benefits as well as improvements to manufacturing technology over the last 50 years, yet both are Sea-Dwellers... one just might have COMEX written on the dial whereas the other doesn't.