I'd read the negative comments about the dual stacked knobs for years and years. I figured they just "didn't work right." Then I got a bass with that configuration. I'm not quite sure how the comments above are meaning "pan pot" but there is no way the two volumes on my stacked knob jazz basses work as pan pots. A pan pot is full neck in one direction and full bridge in the other and then the overall volume is controlled by a dedicated volume. I've had plenty of those and that is not at all the way the two volume knobs work on my stack-knob j-basses.
Having said that, it is true that the tone controls do not sound as if they are completely isolated between pickups (easy to confirm with a bit of tinkering around with the controls). However, I don't really care that much. One tone knob certainly isn't going to favor one or the other pickup either. Even though those two tones interact to an extent, what I do get is a "different kind" of roll off of the highs depending on which one I use or to what degree I use both. If I use only the neck tone, it sounds to my ears quite like the effect of a single j-bass tone pot. If I use only the bridge tone, it has less of an overall effect but when rolled off full gives a more "honky" midrange tone than the other tone does. If I roll both of them back full, it gives a super dark tone (like a regular tone knob rolled back, but way more woofy).
But I'm still not quite understanding the "pan pot" comments. Neither volume pans back and forth. They act as any other j-bass volume knobs. It's the tone part that is quite different from the single tone. Given the choice of the two after now having used both, I'd say I slightly prefer the dual tone controls, although it's not THAT much different and having only one tone is certainly simpler. Aesthetically, I think the two stacked knobs do look cooler, though...
Right now, I have two of them: Flea J-bass and 60 RI Custom Shop J-bass. Both are great basses and they sound and act about the same. I actually like the Flea better overall because the neck is almost as sleek as a Geddy J-bass, and I have micro-hands. The Custom Shop is a bit "chunkier" from front to back--but I do love the purple sparkle and gold hardware on that one!