OK, so last night I binge-watched the new videos about it, including the hour-long PMT interview. PH did work with one of the Yamaha luthiers on it and they described that process a little. Mostly what they talked about is how it's not a neck-through but Hooky was ultimately OK with that.
There are, as far as I can tell, three functional differences between the PH signature and a BB734a with a red paint job:
[1] The neck pickup on the PH is a reverse P; on the BB734a it's a traditional P. In principle this definitely should matter, and Hooky maintains this is critical to the sound.
[2] Different preamp. Apparently the PH model uses something more like the original 1200 preamp than the modern one. Again, this is one of the things mentioned in one of the videos is PH working with Yamaha on the voicing of the preamp.
[3] No J pickup, because the 1200S didn't have one.
I will say that Hooky playing the thing in the PMT interview using the original Clone Theory pedal... it definitely sounds like the real deal. And if you've watched any of the PH & the Light videos they've put up on YouTube over the last six months, he's playing the BBPH and not the BB1200S, and it sounds and looks so close I did not realize that was the case (yes, I went back and checked).
The BBPH definitely does not sound the same as my BB734a. Similar? Yes. But you can't quite get the right sound out of a 734a (I certainly can't, but I also noticed a change in sound when I saw PH & the Light live and he was playing a 734a), where the signature seems to nail it. So it's really not "just" a BB734a with red paint on it.
Now, having said that, as someone who already owns a BB734a, I'm not sure the PH model is worth $1200. I mean, as a huge PH fan, sure, I'd love to have one, but as a bass player I'm not sure it's really a good value vs. a 734a. If all you want to do is get that last ounce of the PH sound, great. But otherwise it's not radically different and definitely less versatile.
The PH signature is prettier, for whatever that's worth. Yamaha definitely either has some of the original red paint from the 1200S still around, or they found a perfect match for it. It's a looker, for sure.