The bag stacking feature will be awesome, but you say that may introduce some new bugs.
I think it's possible keeping most features while making bags stackable.

1. make stacked bags unopenable. Only when a bag is unstacked it can be opened. And opened bags with different NBT can't be stacked.
2. Add a buffer slot in every bag-using machine. The processing slot can only store 1 item, and the machine will drag an item from the main slots to the processing slot. Then the item will be processed. Items in main slot can't be processed directly.

1. Doing it that way is rather awkward gameplay wise, which puts opening large numbers of bags on par with the current system. Different NBT prevents stacking already, except when it doesn't, which I have no control over as that's occurring in code I can't tweak.
2. Making my machines work with it isn't a concern, most already can handle stacks of bags with no problem. The concern is other blocks respecting the limits correctly, just look into the issues caused by Mekanism if you want an example of that.