Nothing wrong with making a guitar yours, i doubt I would touch a one off but if you dont like something or think something would look cool then do it, it is your guitar and it is still an EBMM, I am in the process of modding my LE 07 AL to suit me and my tastes.
On a one off or BFR I would only do certain stuff to customize it, such as pickups being changed, different knobs, different tuners, stuff like that. Nothing that would change the paint or anything drastic. If I was made of money though, I'd be buying a couple JP BFR's and getting them repainted as Dargie's. Haha. I'd mod my BFR if it wasn't perfect already.
It's your guitar man, do what you need to. I've routed, re-wired, had the neck shaved down, etc.
But keep in mind if you do something non-reversible (like the above) then your resale value likely goes out the window. So if you can buy something closer to what you need (e.g. making a hardtail into a trem) then I'd do that first.
If we're talking something reversible and cosmetic, then there's nuthin' to lose.
I wouldn't change anything on my Dargie...it takes away from the rare factor for me if I customize something that was a limited run and meant to be the way I bought it.
Now...if it's wrong or not is clearly subjective...you bought it..you can do whatever you want to it. But like beej says...the resale value will tank.
As others have said, its your guitar... do what you will with it.
That said, I've never been one to change anything on my high end guitars (which are all EBMM now that I think about it). I bought each guitar cuz they all had what I was looking for out of the box. No need to mess with that for me.
I was thinking of putting a push pull knob on my JP limited edition 2006 but then decided to wait.
I also spoke to my tech about putting a piezo in, it would cost me 400€ but I don't thinkI'll do it, there's a lot to do and bad things could happen
I love everything about my JP - I wouldn't change a thing. On my White JP I used to have, I wanted desperately to have all black hardware, but the cost and risk were too high. I didn't want to change the tone or botch the bridge trying to have it blacked out...
My old Peavey Predator is a different story. Nothing is stock on that guitar except the wood and the wiring/switch... Everything else was replaced to my liking. I have $500 in a $100 guitar. Haha. It was my first guitar and I would rather customize it than sell it...
The only guitar I have never needed to mod is a MM. I have had a lot of guitars in the past, and always had to change something to either improve reliability, or sound. So far, I have not changed a single thing on my MM. They are perfect!
Do people still do that nowadays?? Or is that too 90's???
On topic: i've changed some knobs, straplocks, and replaced a broken tip switch, that's about it... It's your guitar, whatever feels right to you, do it!