To the OP in general, thank you for your thought-out criticisms, they're interesting. It's always fascinating to see new people and to see what needs concerns and opinions they have, and what issues they have that are consistent with stuff we longtime EA participants have had.
As for the inventory and looting issues in particular, it's my opinion that the reason all the chests and stuff are a problem now are because no part of the looting or inventory systems are inherently interesting to interact with. Count Turnipsome, I see your point but just think that the way BG3 currently handles things is simply bad. The game isn't asking you to make interesting choices with its looting. It basically says "just loot until you're bored." When dealing with inventory, the only question you're asking yourself is "do I want to go through the hassle?" That's not a way to make a fun, engaging system. There's no actual reward. It's not a puzzle where you have to weigh what's important at the moment, it's really not that hard to carry basically everything you want. It's entirely mundane and forgettable.
In fact, I think the overall idea you had about tying highlighting lootable objects to a skill check (probably perception) would be great, minus the tier 0 stuff. I think items should only be trapped if it makes sense that they be trapped, which depends on context. And certainly empty items being trapped is usually silly. Maybe the container was set out specifically as a trap, but otherwise if it's empty then the trap was probably triggered already. But otherwise, your idea would make looting actually interesting. It would require mentally engaging with things, not just mindlessly clicking until it gets too annoying or boring.