The stock wiring on an older (probably pre-1987 or so) Series bass is set up with stereo output on both the 1/4 jack and on the 5-pin Cannon connector. The audio outputs on both connectors are exactly the same. Three of the five Cannon pins are the two pickup audio hots and a common ground. The other two pins are the external power supply which I seem to remember is around 30VDC.
When you stick a plug in the 1/4 jack it turns off the external power and switches on the two 9V internal batteries. The Series electronics are optimized for performance, not low power, so a set of batteries will last only 10s of hours instead of the hundreds or even thousands of hours you see with EMGs and other active pickups.
All that's in the floor or rack box is an AC->DC power supply and a simple switching system so you can get the individual pickup signals or a mono blend of the two.
On later Series basses, the 1/4 jack is a mono out. It still does all the switching of power supply, but you can't get the individual pickup outputs there, only on the Cannon connector. This is generally a good change I think - in the original configuration, a regular guitar cord will give you only the output of one pickup which means you'll need an adapter to use the bass with a wireless transmitter and you're also hosed if you don't have your special cables in general. When you have a new instrument built, it looks like you can pick old or new style and even the option of having a stereo/mono switch on the 1/4 jack.
The outputs on the 5-pin connector are unbalanced signals, just like you'd find on the 1/4 jack. Even though the Cannon connector is used, they're not balanced, so you're not missing out on anything there. The output on both 1/4 and Cannon are low-impedance since everything going through active buffering amps in the in the internal electronics.
So, you're not losing out on anything soundwise without the external power supply box, but you should make an adjustment on what you pay for an instrument that's missing this stuff. If you want a replacement box and cable that must cost between $600-1000 from Alembic, not a small amount!
David Fung