Thank you for the answer.

That makes sense to not have runtime fluidboxes tied to the prototype they originated from.

Is it possible for a runtime fluidbox to have read only access to its "pipe-connections" (the array of "FluidBoxConnection") parameters? I'm not sure how the game deals with ...

entity.fluidbox.get_prototype(index) should return the fluidbox prototype used by the fluidbox that can be accessed by entity.fluidbox[index]. Instead, it returns the nth entity prototype's fluidbox definition (eg, if index = 1, then it returns the first fluidbox defined in the entity prototype ...