Most of what you post, EM, is how things are discussed in vintage guitar circles, grounded in fact with some hyperbole and myth tossed in.
I spend a lot of time in this world. I’ve owned a few 50’s guitars including a '57 Gibson Les Paul Special and other old, desirable electrics. I currently have a few old acoustics, Martin’s from the '30’s and a Gibson from the '40’s.
Joe B is this generation’s Rick Nielson (Cheap Trick): grew up in a music store, made it, and has a collectors jones bigger than Texas. When Joe scores a real find, or adds to his burgeoning Les Paul sunburst collection, it makes news. This V got a lot of reporting.
The V is “Amos” - named after the owner of the music store in Indiana, Amos Arthur, who got it as a curiosity for his shop window. Story here: The Story of Amos: Joe Bonamassa’s ‘58 Korina Flying V | Reverb News. Back in the day, Ted McCarty of Gibson was looking to compete with Fenders modern designs. So G came out with the V, the Explorer (originally the Futura and a tad different), and never made a third model, The Moderne. Only about 100 of the V and E were made each and they sold really poorly. They were bought as props and curiosities and went nowhere.
A few bluesmen like Lonnie Mack and Albert King got them. But until glam rock in the 70’s they were no big deal (Hendrix played one that he had painted).
As for why a guitar is valued so much - V’s are n the $300-$400,000 range - it is a combo of factors, but clearly is anchored on the fact that our heroes played them and they are scarce. With only 1,800 sunburst Les Pauls made from '58-'60 and the fact that SO many great players used them at one time or another and there ya go.
I’ve played a bunch of them - only a couple of V’s and Explorers in shops, but a few Les Pauls and many, many old Strats and Teles. I love old guitars and always say that an older example of an excellent guitar tends to sound better than a new equivalent. Some of these old guitars are Truly Special.
Having said that, we are in a Golden Age. We have figured a lot out and, IMHO, with great electrics you really can get a similar tone. After playing many, and living with a few great old guitars, I assembled a couple from aftermarket parts based on what I learned and sold my old guitars. Or, rather, I shifted my Guitar Toy Budget into old acoustics. They sound different and obviously superior vs new guitars to me, and I don’t think I can assemble a guitar similar to my prewar Martins from aftermarket parts.
That won’t stop the market for these older guitars.
OP, hope that helps. If you have further questions, I can help where I have knowledge.
ETA: here’s a famous clip: Guitar World reveiws the new DiMarzio PAF 36th Anniversary - YouTube