I heard the opposite, set necks are better, and neck thru body is the best. I think it's just one of many variables.
After I bought my PRS CE24 I saw a video of PRS himself saying that the maple bolt on neck was different than a glued in mahogany neck. He made the point that one of the reasons you glue a mahogany neck is that the wood is soft, and the screws will strip out over time. Maple is hard, so you can safely use a screws to attach a maple neck, at least according to PRS. But then he probably knows a few things about guitars, and what he didn't know Ted McCarty probably told him.
There was an old 3 part video interview of PRS where he answered the question about tone wood, and finish, and stuff. He said, yes it all matters, to one degree or another. he said the sound of the guitar is the sum of all the things that go into it. To show that he held up a block of Honduran mahogany about 12 inches long and 3"x3". He suspended it from the end in a hanging fashion and struck it with a knuckle or a small hammer, and it rung out like a bell, and kept ringing for a very long time. It was an amazing demonstration of tonewoods.
My guitar teacher sold his real '65 SG, and replaced it with a bolt on SG. He said it good enough, that he didn't feel too bad about having to sell the '65.