Brad,
When I initially began the process of ordering a custom, I had a wonderful conversation with Susan about this. Apparently, back in the day, they did not save all their templates (though they do now). This was the case with John Entwistle's Spyders. I own a Spyder, but I wanted one like his, or as close to it as I could get. One look at a picture of his basses and you can see that the Spyder Limited Editions and those he played have different body shapes. I can't explain why the Featured Custom page states what it does, but I do know that the great people in Santa Rosa did the Photo Shopping necessary to get the body right. To wit, the upper horn meets the neck further up, the cutaway is a bit deeper, and the bass itself is thinner at the waist, if you will.
Susan told me each bass they made for John was slightly different, so if there is variation in the body shape, this might also be a reason for it. I do know, for example, that John's V head Exploiter had the long tailpieces that are similar to those on my Spyder; the one's on others were much shorter (I'm having these recreated for my bass as I'm cramming a bunch of Series II electronics into the body; I need all the room I can get!).
I'm only speculating here, but I'm sure Alembic had good reasons for any changes made. I'm sure a phone call to Susan or Mica would clear it up if you're so inclined.
Alan