the passive volume, blend and tone pots do make a difference on sound - the values and also the way the taper on the blend work. There is a difference in sound for if you use 500k pots or 250k pots - one will sound a bit brighter, the other a bit darker. Its not hard to imagine that John East picked a slightly brighter sounding set up that would work with humbuckers and single coils - knowing that the passive tone could then correct it if it was too bright.
Ibanez have chosen values based on cost and that work with the preamp. John East has been able to design a completely separate passive path and optimise it how he wants.
If I gave you two basses, one of which had a slight bit more going on in the top end, it's not surprising it would sound better!