Neckthroughs have a ton of advantages over bolties IMHO:
1) less susceptible to "rising hump" on the fretboard
I've never noticed this in any of my boltons, so I'm not exactly sure or what you are referring to here. Are you talking about a bump arising due to a heel adjuster tross rod?
2) better sustain
This point has been argued to death and I'd have to say I've owned both and I've had clunkers with no sustian and great bolt ons with tons of tone and sustain. My Mahoagny MZ Charvel for instance has tons of sustain.
The fact is though it really doesn't matter a ton because of the high gain amps most players use now. Unless you are playing acoustically or drastically low I doubt seriously that you would notice THAT much ...
Lastly on this subject Neal Moser some time ago did a post stating he believed neck woods played a huge role in the tone of a guitar, more so than body wood. The theory was that most of the resonation comes from the vibration of the neck as is is much thinner. This is something I've noticed in varying guitars IE: Birdseye necks VS Quarter sawn or even the Eastern hard rock maple used in the old San Dimas Charvel VS the Maple used in the model series. imo the woods are each a very different density. I'd tend to believe that plays more of a role in sustain and tone than bolt vs neck thru
3) better access to high frets because of a slimmer heel
Not always true, guitar manufacturers have gone the route of doing recessed and taper heels to counter that. While you will never get the same transisition that a neck through has you can get a countoured heel that is much more comfortable than those of days past
4) neck never misaligned on body
Can't argue that point at all. But what I can tell you is that you have a better chance of aligning a misaligned neck on a bolton that a misaligned (Factory) neck on a neckthrough... I believe that would require a new guitar to be built... Yeah I know impossible right ...Jackson never makes a mistake
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5) Cannot have bogus neckplate and S/N (ok so that doesn't really apply much in this case)
Yep another great point, I guess it would be really hard to buy a set of 1/8" metal stamps and change numbers or forge numbers on a fake neckthrough. While it isn't as likely it isn't as hard as you would think to do that ...
6) Can paint in a way that flows into the body
Not sure what you mean by this one .. What I can say is that it is much easier to send a bolton body for paint because you don't have to ship an entire guitar ..
7) Usually don't develop neck pocket cracks in finish
Nope you are 100% correct on this one but lets be fair here. It doesn't impede playabilty and usually it isn't very visible. Most boltons will usually deleop this problem but unless you are looking for it then it really don't stand out and doesn't normally hurt the guitar.
8) No neck plate to interfere with strap button placement
The only guitars I remember having a strap button placed on the neck plate were the old Stars. I'm sure there have been a few others and Jackson pros would know that more than I would. Warriors? Kelly's?
I've never had a problem with my neck plates interfering with my strap buttons placement on my strats that I know of ...
The bottom line is this age old argument comes down to preference and beyond that there isn't a whole lot of wiggle room. I don't believe either option has it 100% over the other ...
You could make the case that if you have a neckthrough with a back bowed neck it is junk vs a replaced neck on a bolton. Or the fact that a lot of gear heads love to mod their guitar and can swap out dfferent styles of neck easily. If you prefer oil vs paint unless you are getting a custom shop neck through you either have to find it as a rare option or strip it yourself ... etc ...
Marty Friedman - neckthru Kelly
Steve Vai - Soloist
Randy Rhoads - Concorde
Jeff Loomis - neckthru Rhoads
Alexi Laiho & Roope Latvalla - neckthru Rhoads
Zakk Wylde - neckthru Rhoads
Vinnie Vincent - VVV
Troy Stetina - Soloist
Kirk Hammet - neckthru Rhoads
Buckethead - custom King V
Rusty Cooley - 7 string Soloist
Are Kurts esp's bolt or neck?
How bout
Steve Vai "Green Meanie or his Jems"
Warren Demartini
Jake E Lee
Paul Gilbert
Bruce Kulick
Satriani
Eric Johnson
Yngwie "unleash the fookin fury" Malmsteen
Nuno Bettencourt
EVH
George Lynch
etc ..
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