Perhaps they should use a system of looting where you only loot materials or old busted items that need to be scrapped in order for you to create a usable version. For example, you open a working stiffs crate and you find inside a low quality iron pickaxe, which when scrapped gives you a small amount of materials for you to eventually craft your own. The quality that you craft should be dependent on your skill as a craftsman. The chance to find a working tool or weapon should be based on the difficulty of the POI you're at, but generally this should be somewhat rare, so maybe only a few POIs would have this. This feels most logical for me when you try and think of a narrative for this game. You're a survivor with no experience in a zombie apocalypse, you need to slowly gain experience in all aspects of surviving, crafting, etc in order to become a more efficient survivor. A lot of it should be dependent on you as the character and not an artificial loot limiting mechanic via gamestages which are technically dependent on your skills as a survivor, but it's still a very artificial approach.
To summarize, I haven't thought this fully through, but maybe being able to loot only materials/parts/items that will be scrapped for parts due to them being rusted from laying in a box for too long could be an option. Also as mentioned above maybe different quality crates should exist, so low tier working stiffs, mid, high, exceptional, etc. I don't immediatelly see any negatives to a system like this.
I think this game should have a mixture of arcade and realism. I enjoy it being somewhat lighthearted and not full fledged realism like dead matter for example.