Re: Set-Thru or Neck-Thru-Body?
"lost" probably refers to the diminished role the body sides play in the overall electric tone. The neck block (usually maple) governs the body vibrations to a much greater extent. It's not bad, I just prefer it when the bridge of the guitar is surrounded by a large mass of body wood. So I make deep tenons instead. But it's personal. I don't have an agenda, or think it's better.
To me the "low end spike" is actually a high mid muting. It's a net reduction in resonance, not a spike or boost. The NT construction combs away the open, upper midrange (that agreeably sometimes makes a guitar sound thin or bright) you get from a bolt on. Acoustically, with otherwise similar guitars, strumming a bolt neck unplugged will be louder than the NT. But that means more energy is being left in the string, and that's not a bad thing.
Traditional set necks are actually totally different from deep sets or bolts. They're not like an "in-between" tonally. The tenon is small enough for the glue joint to stifle the vibrations from both pieces, but not enough to really transfer neck vibrations strongly into the body. Again, not a bad thing at all, millions of LP's and other guitars can't be wrong.