One thing that everyone making a JB-4 (and the variants of) has to do is fill and re-rout the fixing lug pockets for the pickups if they want to fit any after-market replacements. It also requires getting a new scratchplate.
Could you talk to the factory and see if they can find some standard-format pickups to supply with the kits in future, plus modifying the pickup routs and scratchplate to suit? It would make the upgrading easier for everyone and I'd bet that you'd sell more JB kits as a result.
Not everyone wants to take the time to fill and re-profile the lug pockets, though I'd bet a lot of people would like to fit their choice of pickups. If they'd checked on the build diaries on this forum, they'd have seen what was involved and a lot of people would be put off.
Cheers.