I believe the material storage upgrades probably work by giving you multiple stacks and just showing them as one summated stack per item in the UI. It works fine because the material storage panel has fixed locations for each item, so they can have this different behavior.

Doing that with variable inventory slots that can be anything would require a whole new layer of coding that wouldn't really be worth the effort. Having to right-click:consume-all on two or three stacks if you've been saving something up is a pretty low priority issue. That same amount of labor could be put into something like a keychain system instead, and yield a high a much higher QoL improvement.