Jeff mentioned it recently as well as a couple others over time. @KaraQ said her Epi had the same spacing as her VP, which is as close to original as any Gibson Thunderbird. Possibly someone will have shown documentation or some kind of confirmation. I can't help, and I may have the year or model wrong. Someone please correct anything I may have wrong.
I sent Gibson an email. We'll see if there is a response. I emailed a guy there once and he replied, so I may try him if I can find that correspondence. I think you may very well be right about the change. There is a reason. Possibly the what they redesigned sounded better (awful in the original location). Maybe they were going for a deeper and more clear sound (artist suggestion?), and that just worked. Please keep in mind I'm not saying they sound bad, though it may come across that way, rather it's not what I'm used to in a Thunderbird sound, and that has at times been frustrating. Imagine a long-time Pbass user finding a new Pbass with a redesigned and relocated pickup. It will sound different from the tone one loved for years. Those having never played the old Pbass don't really have that point of reference. I think the second gen Pbass sounds better, in part due to the pickup being farther from the neck.