Jackson's are true electric guitars to the utmost extent. Jackson's are not strum-around-the-campfire guitars. They are made for high volume, high gain, high clarity, high articulation, and stage presence--pertaining to their sharp looks and outstanding paintjobs.
Think about the era in which Jackson's were made famous. These artist's were all about excess--onstage and offstage. They wanted unreal sustain that came from high voulme and more gain. The high output pickups helped push any amp someone was using back then. They still wanted to maintain clarity of notes at high volume, so they had ebony fretboards that made every note come through in detail and it was applied to a thinner maple neck (not to mention neck-through, though not always) that has a very tight, focused, and fast response--thusly increasing the clarity. Apply that to liquid sustain from both axe constuction and overdriven amplifier and you've got yourself a perfect electic guitar under those circumstances. So you can't blame any lack of tone on the Foyd Rose or the routing. Anything you feel you lose from those to things acoustically will be forgotten once you've blasted through a half stack and the sustain is superior.
Jacksons tend to sound cold as bleep acoustically, but that's because they were designed for any high volume assault--which results in a sound in and of itself.
Jackson's were designed much for the technical aspects that some music requires. It wasn't designed to sound beautiful by itself just to have barre chords played on it at low volume. It was meant to be played all out through a high gain amplifier! I mean, you don't invite the "Macho Man" Randy Savage at his peak to a tea party do ya?