Everyone has an opinion on signature guitars but I have no problem admitting I love them because I'm a fan of the artists they were designed for. If they meet the specs I'm after its a win-win. As far as if I'm going to alter them in any way, it really depends on if its going to affect their value and if so, by how much? Pickup and electronics changes are reversible, so not a big deal to me. If I need to changed something beyond that, its probably not the right guitar for me. Here are the ones I've had so far and what I've done to them:
Tony Iommi SG (epiphone) - ended up not liking the signature Gibson pickups so I swapped those out. This did affect the value of guitar but it was an inexpensive guitar to begin so I didnt; lose too much there; I ended up making money by selling off the signature pickups in the end.
Dave Murray HSH strat - I could not gel with the vintage bridge and felt altering that would negatively affect its value so I left it alone and sold it. (although I wish I would have kept this one as they are quiet the collectors item now).
Jeff Waters Flying V - Was a cool guitar but I didn't have it long enough to tinker with. Flipped it to fund another guitar.
Jackson RR1 - not sure how much of a signature guitar this really is. Its kind of like how a Les Paul is a signature guitar. I ended up putting a YJM pot and new pickups in which did not affect its value in any way upon selling it.
Jackson Adrian Smith - Installed YJM tone pot, disconnected tone control, added a D-Tuna. All reversible if I ever decide to put it back to stock configuration and sell it.
Need pics of these sweet metal machines!
To answer the original question, I echo those that say the signature model may have unique specs some of us want but we don’t necessarily care about the guitar being somebody’s signature.
I used to be against them but now I own two. A Kirk Hammett KH-602 because it’s neck thru, high quality, and came with the new bone breaker pickups ($200 EMG), and I bought a fender Chris Shiflett because I liked the look, the standard sized humbuckers, the 12” radius rosewood board and 70s style tuners. I may mod the Shiflett tele at some point. No need to mod the KH unless I want an original Floyd rose on it.
Am I a KH fanboy? A little. Am I a fan of the foo fighters? Not really. Just like the guitars but haven’t modded them.