I used a Nordstrand quadcoil MM humbucker in that body when it belonged to me, and like you, unless the pickup was split into single coil mode, the passive tone roll off doesn't really work as expected. It kind of makes the series humbucker sound more middly and nasally, instead of warmer like it does with a split P pickup -for example.
However, since then, I have built another Warmoth with the same pickup placing and passive controls because I can't do active basses anymore. Something I did with both that purple body and my present Musicman/Jazz hybrid is put push / pull CTS pots in the two holes and like this I can access: front single coil, back single coil, both in series, both in parallel. Just from the two hidden switches.