Bell is assuming that:
- Alice's results in region ##A## depend only on facts about regions ##C## and ##E##.
- Bob's results in region ##B## depend only on facts about regions ##D## and ##E##.
He is also assuming that Alice's and Bob's settings (their choice of which orientation to measure spins relative to, for example) are
NOT determined by the common backwards lightcone ##E##. For example, Alice might make her choice based on information about region ##C## and Bob might make his choice based on information about region ##C##. Bell is basically assuming that there are facts about those two regions that are not deducible from facts about region ##E##.
So in this setup, the "hidden variables" are just facts about region ##E## that causally affect regions ##A## and ##B##. Any facts about region ##E## are fair game. Maybe it's the values of fields in region ##E##, or maybe it's facts about the particles. Bell's theorem doesn't depend on the nature of those facts, only what region of spacetime they are about.