If I understand the description correctly, the input and output pitchers are side by side, on the same level. In which case, how does the fluid get from the input pitcher into the machine? The way you describe it, the contents of the input pitcher have no mechanical way of being removed. Teleport maybe?

Output is simple, a spigot above the pitcher. But perhaps some sort of probe or syphon for the input side... or the pitcher has an trapdoor-like base that seals watertight. (sort of like those beer glasses that fill from the bottom up, but in reverse).

Either that, or I propose an alteration. Input is through a removable disposable plastic hopper at the top (for all the reasons you list about contamination) that can be unscrewed and replaced. Output is water on one side, and dried dehydrated stuff on the other. That way material flows through the machine. This way the containers are irrelevant to the operation of the machine. water comes out of a spigot on an arm that pops out when it's ready, so it can fill any sort of container. Dried stuff comes down a chute... say on the other side of the case, and what it lands in is whatever you have to hand.