Jake,
Thanks for your support in both my cheating and my spin on JT's bass parts.
He certainly is a great guitar player. One of the things about playing with him is that he's already playing all our parts - including the bass part. When he plays the song by himself everything is there, he doesn't really need us... So he essentially writes our parts while writing the tune.
What's left for us to interpret are decisions like which octave and how many pushes to catch with him. (He tends to play the bass note with his thumb as a pickup to the chord which falls on the downbeat. Cutest example of this is when cuing a final chord, he can't help but sound the bottom note before the band comes crashing in.)
Another admission here; although I've played fretless on at least one tune of each record I don't bring that bass on the road for the live gigs. Part of the reason is that I am always doubling JT's bottom string and if the sound on stage is not ideal it becomes very difficult to match his intonation, and that can just get ugly! Also, when I first joined the band Carols Vega's sage advice was don't make the gig harder than it needs to be. And furthermore, I've been to many shows where the bass player changes basses 10 times and I simply could not hear any difference from the audience side of the PA...
So those are the forces which shape the JT bass parts. It may sound like a stifling musical situation to some but I dig the challenge of playing the right note with the correct dynamic at the exact moment consistently every night. That's enough to occupy my wee brain!
I'm not sure what you mean by 'possibles' but I'm guessing you mean alternative notes or extra bits? There are a few moments here and there in James' set but I tend to concentrate on being exact as opposed to changing things up, again partly because I'm just doubling him. The other members of the band are better at altering things and the instrumental solos are open and different each night. I save that kind of thing for my other gigs. (With Holdsworth it's like a year-end sale all notes must go! Ha!!!)
Jimmy J