I just listened to both through my studio headphone/monitors. Most obviously a difference, it sounds like the vintage neck shifts the resonance frequency down in comparison to the modern neck.
I have a maple fretboard version of the vintage neck on my MIA jazz. I think it sounds great, does not have that mid-bump that's evident in your recording.
For the bass in the OP recordings, I would utilize the modern neck. More usable of a sound/tone to me
MIA Jazz, Les Paul Bass, VM J-5; Basis M-2000, Eden WTDI, Powerhouse 215 EV, Fender PRO 810