I hope this should be easy to do as it’s similar to how the engineering borg handles wires, and the medical Borg handles topical medicines.
Have the containers act in the same way, right now the advanced medical borg is unable to put its small beakers into the chem master so if the plasma is in the chem master like it should be, the borg is just locked out from making meds.
Same thing with the service bot. It has a drink mixer but can’t place it into any machines so you can’t serve drinks.
(I know the borgs aren’t supposed to be as good as a player, but the smaller beakers already make things much slower for the advanced medical module, not sure about the service bot but it should be able to do what people expect it to be able to do in it’s description.)