This explanation (and the one about just repeating the 2012 NR pickup layout, if in fact they are the same) seem most plausible.
Keep in mind, the neck dimension changes, the headstock size changes, the bridge changes and the pickup design changes and you’ll quickly realize it isn’t going to sound exactly like a vintage bird regardless of where Gibby put the pickups. So with that in mind I suspect they just visually placed the pickups on the prototype where they thought they looked nice and balanced, then played it a bit a concluded “good enough”. And from just about all owner reports, the sound of the new NR is in fact “good enough” to be called a Tbird. Only a connoisseur of fine vintage birds will be keen enough to readily hear the difference between the new and vintage NR, and even then probably only if they have a vintage bird they can A/B it with. Those folks are few and far between, but a fair number of them are in this club, hence the difference spotted.
Totally old news I know.
Part of the goodness of old basses that we like so much is that they're old and aged.
Been taken care of, (some of them).
The wood has gone through the years in a good way.
Yes, you can reissue/recreate something. And to good standards.
I just don't think most "reissues" come close enough to really represent an original.
Unless you got some magical one off that really sings.