I have been using the 2x2 drawers as a ready inventory. Basically if I am going to the nether I get these items or if I am just mining then I get those.
The issue I am having is that if I put my emerald pick into the box then use it and try and return it to the box it is now a different item to the box because of durability. Also if I have a bunch of the picks in the box waiting to be used, then as soon as one comes out it and gets used it can't go back.
I had looked for a way to hit a toggle for Metadata filtering but I was not able to find it in the interface. Is this something that has to be done in the config files? If so I would like to suggest that it be made a toggle in the interface per drawer module. This would allow some things to be filtered by metadata (default) and others not. If it does not exist can this be added.

Basically, you want a a key to turn off NBT/durability sensitivity? The problem is, that would imply a more fundamental change: From storing X number of fungible (interchangeable) items (like every other drawer), to storing a list of unique items. Consider, if you put your worn Silk touch pick, your Fortune pick, and your newest Silk Touch pick in the same slot. When you ask for a pick, which one do you get first? That would be a big change codewise.

You might just want to go with some combination of item frames, dispensers, and armor stands for this purpose.

I also like this idea. Would it be possible to perhaps do it along the lines of compacting drawers where since you can combine tools to combine their durability that the drawer could auto do that and track how much durability is in the drawer to give you a full durability item whenever you take it out? I have no clue if that's feasible or less complicated than the unique item thing, but it's a thought and it'd come in handy for all those base tool and armor drops.

You know I hadn't thought of the repairing by consuming others, that is a good idea. It would eliminate the worry over which to give. Using that idea, you could have an interface to set the primary (in the case of an item that is enchanted) and it would default to repairing that one first. Probably prioritizing the unenchanted to consume first.

An interesting idea, IIRC Filing Cabinets does something similar with one of their folder types. You'd probably need to block the player from adding a (differently) enchanted item to the drawer.