Could be that since the WoB doubleshots are PBT for both materials, whereas the backlit compatible uses POM for the "clear" part? AFAIK, PBT is a tricky material to work with due to it's thermal expansion coefficient and tendency to warp if cooled to quickly, so the molds have to be designed specifically for use with it.
Also, the PBT in the backlit compatible caps may well be a blend to minimise these effects, so they can use cheaper molds?
All pure speculation, there could be other simple business reasons for it, too, since the doubleshot PBT sets were made first and they could be using the same molds for the backlit sets, but since they have to recoup the costs of the molds from the first sets made with them, the doubleshot sets had a higher initial price set. Lots of possibilities.