Sorry, but Marcus Miller doesn't sound the same with a Squier, a Sire or his Signature Fender, which, by the way, is more a Sadowsky than a Fender. If you've heard and seen him live, he is fighting with his Sire to get a decent sound and doesn't feel at home until he picks up his "Fender" bass.
That said, you can ask Fodera to put the output jack in the headstock, they will do it as long as you pay for it.
What you don't seem to understand is the "philosophy" behind Signatures : people buying them want the exact same instrument, which is an heresy, for sure.
I've been playing luthiers basses for years and, again, sorry, but I really can't play mass production instruments anymore.
But again, the best bass is the one you like, be it a Squier or a Fodera.
That said, except the AJ6, I don't like Fodera's at all : way far too expensive for what they really are.
My main basses are Leduc's because they are just what I'm looking for.
And take the time to listen to Anthony Jackson.