I cuncur about 90% in regard to where you're coming from Joe. I too can see where the value of, say, an airworthy SBD Dauntless from Lake Michigan would far outstrip the same plane's value in "as recovered" condition. That said, if the same plane had somehow been found mostly intact (in fresh water, miraculously

) where it had fallen following the attack at Midway for example, its historical value would far outweigh it's value as yet another remanufactured warplane populating the circuit.
On the other hand, if Amelia Earheart's Lockheed 10 was found mostly intact in the jungle, I think it would be ludicrous to rebuild it from the ground up just to tour it and thrill airshow crowds. Michael Jackson being rich enough to completely rebuild it and paint it pink by personal preference would in no way make the act any more justified. There IS a threshold where an aircraft's intrinsic historical uniqueness makes it more valuable as an artifact rather than a generic template for manufacturing the "ninth airworthy example of its general type". That can be done without destroying one-of-a-kind artifacts in the process.
Depending on the new owner's resolve to maintain originality at all cost, the relevance of Dottie Mae's paint scheme following it's restoration to airworthiness might as well fall to a coin toss. Any man with the financial means could do the same with nothing more than a legible data plate and a few surviving castings and minor components. That's all that is destined to remain of Dottie Mae in the end any way. Why break up what is otherwise an astounding historical touchstone to achieve the same goal? Other than the story itself, most everything you see in those photos that excites you is on a slow road to the scrap heap.
I can use the restoration of P-38 "Glacier Girl" as another example. The one thing that has made THAT particular aircraft so historical is its recovery and the restoration itself. Without that, the plane was just another anonymous Stateside fighter who's greatest historical accomplishment was rolling off the factory floor. It's current situation far outstrips the relevance of that, even though she's all new metal for the most part. After all, there are still five other P-38's that share her same exact history still preserved beneath the ice! Just like the Lake Michigan SBD's, she's nothing overly special without the "recovery and restoration" chapter in her history.
This P-47 is the ONLY Thunderbolt you will find on this planet that remains largely intact, just as it was when her squadron was changing the course of world history. She may well be the only Allied fighter to survive in this undisturbed original condition (as far as I know). Her uniqueness and originality is unrivaled among museums, yet I'm supposed to believe that somehow tearing her apart for patterns for making a new-production, airworthy example of her likeness is supposed to trump the very history that made the Thunderbolt the icon that it is in the first place? This plane was at the heart of the action where the type's reputation was forged, yet it might as well be serving as the basis for the next bitchin' Reno racer.
Maybe I've been spending far too much time attaching value to actual WWII history and not enough time honing my praise for those rich enough to recover a one-of-a-kind historical artifact, only to effectively destroy it in the name of "flight at all costs". If another restorer locates the data plate for Don Gentile's P-51 Shangri-La and fabricates a new plane around it, I would hope the man representing "Dottie Mae" would not presume that the aircraft under his own butt is any more historically relevant. Other than that, I suppose I'll be happy enough knowing the story of this particular Jug will now live on among enthusiasts rather than be lost to time.
By the way, I hear the Crown Jewels are for sale on eBay. The man selling them actually bought the lot and replaced them all with exact duplicates before destroying the originals. Still, his actions are now part of the written history of the collection, so he and other experts feel the intrinsic nature of the jewels themselves should still be considered largely intact. Some have questioned the actions of the new owner, but people should realize that it is "his" collection to do with what he pleases after all. Any takers?