You may as well ask why anyone chooses any component, speaker, amplifier or effect. You can carry it further to neck construction, wood selection, string gauges, materials, and construction.
It's all about the sound and feel you're looking for.
Though I'm no Garcia biographer, Jerry must have been playing guitar for over ten years when Alembic pickups came on the scene. By that time, I suspect he had developed some sense of how things should sound. Look at the trouble some people have today when they get their first Alembic guitar. I recall a variety of reports from people that their effects didn't sound right with the Alembic as compared to their previous normal pickups.
In any case, we can all hear what they sound like today and make our own decisions about the sounds we're looking for.