From the article, here's MJ's take on the JB controversy:
“I don’t know magic, but it could be one of three things: We changed from the long-legged bottom plate to the short-legged one. [Ed. note. This was primarily to accommodate shallow pickup-cavity routes.] We also used to use butyrate bobbins like the ones in old PAFs, but at some point the vendor didn’t have the material anymore. Also, our old magnets used to be rough-cast, but then somebody switched vendors.” Standard JBs are now made with ground magnets, polycarbonate bobbins, and short-legged baseplates.
But Juarez is quick to add that those components might not even factor into the sound of those old JBJs. “It’s mainly how you wind those bobbins,” she says. “The trick might be in winding it kind of tight. That’s why we still have our handwinding machines in the Custom Shop. We have the scatterwinding machine, and we have one of the newer machines. We know that a pickup wound on the newer machine is going to sound different from a pickup with a scatterwound bobbin.”
Even allowing for those differences, Juarez insists there’s too much mythology surrounding the JBJs, and she plans to conduct a shootout between the three different versions. “We’re going to do a sound test,” she says. “I intend to compare one of the old JBs, one made the new MJ way, and a regular production model. It’s on my to-do list.”