I am a musician, not a collector, and I do not care if a new bass has a poor setup any more than I expect a new car to be delivered to me with the lights, mirrors, and visors adjusted to my preferences. And that last comparison is one I have shamelessly stolen from someone else here on TB. So to me the definition of "the real thing" comes down to whether or not the company is still making products for real musicians. All the Fender and Squier basses I have tried lately show clear evidence that they are made by a company that does care about musicians. They aren't all perfect and since I have not tried every single available model there may be exceptions. Yet the ones I have tried are honest efforts to satisfy some musician or another. I don't know of any real reasons why I would prefer to play a 1960's Fender over the ones I have. I have no desire to own a pre-CBS Fender. As it happens I only own Fenders at the moment but I am sure that many other storied brands that have gone through their own corporate twists and turns over the years are also as genuine today as when their founders first picked up a piece of wood with the intent to make an instrument. No Fender ever was a Stradivarius and I don't think any boutique bass of today, however finely crafted, is either despite the claims of their builders and fans. They are electronic instruments, they don't need to be Strads to sound great!
Collectors are another breed. They collect what they collect, they value what they value, simply because they do. They can't always explain why they do what they do and I probably don't want to know!!
Ken