I think adding another tier to make the itemduct move stacks or perhaps an upgrade like how extra-util's transfer nodes are like.
I would think the upgrade would have to come at the inventory connections, else you would have to make it so ducts of a different tier couldn't connect to each other. Or you could get inventive and say you can move stacks at a time but items move much slower, and upgrading to glowstone ducts mitigates the speed penalty significantly.