I think it would be pretty hard to exactly replicate the Series design with other pickups. It has to do with the way the pickups are constructed, and some explanation is in order.
First, start with a single coil pickup. You make that by winding a coil around a magnet and disrupting the magnetic field with something like a vibrating ferrous string. The magnetic interference has the effect of generating a electrical signal in the coil, which you can amplify to reproduce an analog of the strings motion. You can tweak the sound of the pickup by varying the strength of the magnet, the shape of the magnetic field (this is the aperture), and the type and amount of wire on the coil.
The problem with single coil pickups is that in addition to picking up the motion of the string, they also will pick up radiated electromagnetic (EM) fields, which you hear as hum and buzz.
Humbucking and humcancelling pickups cleverly address this problem by using a matched set of pickup coils. If you reverse the polarity of a single-coil pickup magnet, you'll reverse the polarity of the output signal. You can also reverse the polarity of the signal by reversing the direction the coil is wound in. If you flip the magnet AND wind the coil in reverse, the pickup should sense string motion exactly like the regular pickup does.
But picking up an EM/hum field doesn't depend on the magnet, just the coil. If you hook up a regular pickup and a reverse pickup, what will happen is that the magnetically-sensed sound will add normally, but the EM-induced buzz (which isn't dependent on magnetic polarity) will add up out of phase and will be cancelled out like magic. This is how the two coils in a Gibson-style humbucker are wired, or the two halves of a P-bass pickup. In modern Strats, the middle pickup is reverse-wound/reverse polarity which is why the in-between tones don't hum.
In something like a Gibson humbucker, the two coils in each pickup have magnets and hear the string in slightly different places. This means that the audio outputs from the coils are slightly different and that small difference causes some additional out-of-phase cancellation of the audio signal. That's one reason why most humbuckers are less bright sounding than single coils.
One way to reduce the amount of high-end cancellation is to stack the two coils one above the other. It works the same as side-by-side, but both coils are pretty much seeing the same string motion now. The problem with this design is that one pickup is farther away from the string, so you still don't get a perfect signal match (the closer pickup will have hotter attack for instance, so the summed signal won't be a perfect match). This is how stacked Strat pickups work.
If you're willing to dedicate one coil to hum cancelling only, then you can perfectly capture the single coil sound by leaving the magnet out of one of the two coils entirely. The coil with the magnet hears the string, and the air coil only hears EM which it will cancel out of the other signal. This is what the Series bass is doing. The pickups are true single coils; the hum canceller (shared by both pickups) is a coil with no magnet which only serves to remove the hum when summed with the pickups. The EM/hum radiation is basically going to read identically anywhere on the instrument, so, with proper matching, you should be able to perfectly cancel the hum with minimal effect on the single coil sound.
I'm not sure whether the Fatboy is a stacked humbucker or whether there's a pickup on top and a humcancelling coil beneath. In either case, there's some compromise vs the Series setup. If it's stacked, then it's an issue of coil imbalance. If it's an air coil humcanceller, then the problem is that the proximity of the air coil to the magnets of the pickup will cause some weaker signal to be induced again mismatching the outputs. That's why the Series humcanceller is physically located away from the pickup magnets.
Whew!
A couple of additional observations. First, Leo Fender was pretty clever in making the split-coil P-pickup. By making it that way, you can build a one pickup bass that doesn't hum and doesn't have high-frequency cancellation (only one coil reads each pair of strings but together then cancel the hum). Second, if you can pry the magnets out of the middle pickup of your Strat and do a little rewiring, you'll have the purest, humfree neck and bridge pickup tones you've ever heard. I'm surprised that you don't see more Gibson-style humbuckers with a live coil and an air coil, but I guess that doesn't sound at all like a traditional humbucker.
Finally, this is a great example of Alembic's no-compromise design. There's lots of ways to get pretty good results, and only one way to do it that's ideal, and that's what you see on the Series. I know of only a few other basses that have this system - the original Paul Reed Smith basses had an extra hum-cancelling coil on the back, and there was a short run of Fender Elite Jazz basses that had this in the 80's. Alembic was first on this (certainly the first significant player) and never stopped since the 70's.
David Fung