I just read your review, and coincidentally I read it the day after I 1/2 aired my vintage Tone Zone. Your finding that the factory AZ still contains the spacer and so is a 1/2 aired TZ came as a surprize. Nonetheless, your detailed comparision discription is spot on to what I am observing. You nailed it.
I had to change the pickup height settings and the pole piece adjustments slightly to get back to the sound I liked so much in this guitar all these years. This would seem to confirm your thoughts about resonate peak differences.
The reason I decided to try the 1/2 air mod was because of the lower mids congestion. With this guitar I play mostly single note solo stuff and I always loved how the TZ made singles notes played up higher on the neck not sound thin, but still have a PAF vibe. But the lower mid congestion always made chord work a little less than ideal. I can run it in parallel and it clears up, but then series works better for an overdriven solo tone. It's kind of PITA to switch back and forth. The difference between the stock TZ and the 1/2 aired TZ is subtle, so I don't think I will need to go to the hasle of reversing the mod. It's a win win.
Btw, I did try the AT1 before trying the 1/2 air mod on the TZ. Nope. Hated it. I don't want to disparage the AT1, it's a good pickup, but it has no PAF vibe at all. And its so dry. I will take a TZ or an AZ, for fat plus PAF type tone, thank you. I have kind settled into the PAF tone area for all my humbucker equiped guitars, and I love the 36th B, but for this rather bright guitar I need a little more.