Back in the early days, Bill used the same epoxy potting compound to pour his pups as Alembic used. We all did, because it was over-the-counter and nobody made the better casting materials that came later.
If you look at the earliest black Hi-As, you'll notice they're quite glossy; the matte texture finish material came later, still.
But so far as I know, Bill never made pups for Alembic. Certainly, no instrument that ever went through Brady St. while I was there had factory-installed Bartolinis in it.
That said, we did do a few experiments with a few of Bill's units to see how they'd interface with the PF-5 and 6 setups. No match at all; we had to virtually rebuild the preamp front-end to get it to even sound remotely musical. And it never sounded good.
When Lane Poor was working at the shop, he did a few designs that matched up electronically with the PF-6, and sounded okay, but he was looking for a different aperature arrangement and never built a set with a shell that would fit a standard Alembic bass. (IIRC, he was trying to see if he could adapt the Alembic system for use in a Jazz Bass, long before Ron designed the narrow aperature setup used today.)
On the guitar Dela remembers, it was definitely a swap-out, as we probably did it at Brady St. We did that once or twice; strip out the standard electronics, send the guitar up to the factory, where it was re-routed for standard humbuckers, then we'd install hot-rodded Gibson HBs and standard Clarostat pots. Some people found the factory setup to be too clean for what they were playing, and wanted more of a Les Paul sound. Usually, we talked them into trading the Alembic in for an actual Paul, then resold the Alembic to someone who appreciated it.