I think a lot of people aren’t too wedded to the vintage specs; they just want a fun bass to play. It’s not like a ‘66 (let alone ‘70 or whatever) Mustang bass is like a holy "1959 Les Paul" or something. It was the student model back in the day, and a lot of us have never even played a vintage one to know what we might be missing.
Personally, I like the vintage specs except I’d take a 9.5" radius fretboard and a C neck if spec-ing out my dream Mustang, and I wouldn’t blink a second to apologize for the non-vintage correct neck.
I’m not saying you’re "wrong", btw, just saying that people do dream of different pickup setups and I’m glad Fender’s finally having some fun with that with the Mustang and its recent Pawnshop, PJ and now American Performer variants. And now, with the Vintera (plus the JMJ), you have the classic Mustang too, for those who want the real deal vintage spec, whether pre-aged or just like new. So now, pretty much every Mustang lover or Mustang-curious or "I’d like a Mustang but I wish it had _______" bassist can be pretty happy.
But I do think, like you mention, the non-string thru option on the PJ was a poor choice and the pickup selector switch was, well, a somewhat odd choice, especially with it compounded by poor execution (a wonky stock switch, ***). Nevertheless, the PJ’s kinda cool. Price is right, classic pickup config., good platform for a little modding, fun like a Mustang should be, etc