When you put a collector limpet controller on your ship, you:
Add a hydraulic or otherwise computer-controlled hatch, on your ship, for dispensing limpets.
Add some sort of row or rolling feeder line which can hold however many limpets you buy, whether it's two or 100, and feed them by computer control flawlessly to the hatch and out the hatch on command. How much does a frictionless feeder line weigh, that can hold 100 1-ton limpets, and feed them flawlessly out a ship hatch into space, on command?
Add some sort of pressure lock to that hatch, or install a mechanism for exposing a variable amount of your cargo hold to vacuum, depending on how many limpets you stock.
Add some sort of loading receiver to the limpet feeder, so that it can be stocked by machine through your cargo hatch.
Edit: Sorry OP.
I forgot that you can selectively eject cargo in whatever numbers you want (I rarely do that).
I was picturing a shell-feeder or torpedo-feeder as on a Navy ship, except commercial-weight, instead of torpedo-weight.
If the limpets are ejected like normal cargo, then my entire argument is void, and OP is correct.
This actually means that our cargo holds can magically juggle and rearrange tons of cargo to the hatch, apparently almost instantly.
I would prefer less cargo-ejection magic, and continued very large weight on all limpet controller mechanisms, personally. A limpet dispenser which takes a variable number of very heavy limpet machines should weigh a huge amount, if fitted into a spaceship. And if I fit 4 tons of cargo into a tight 4-ton cargo space, I shouldn't be able to simply eject one from the rear of the compartment. You'd think that the design constraints for space-faring craft would be slightly different than for Amazon warehouses, as far as volume constraints. Half the valuable cargo space must be taken up by discrete unit management automation.