The whole encumbrance / storage balance question is irrelevant to my personal playstyle, because I’ve never seen a reason to have more than about sixty storage points, which you can get with a backpack and most combinations of sensible clothing. (It’s enough to carry a couple days’ food and water, a gun, ammunition, a melee weapon, first aid supplies, and your everyday tools, plus 20-ish storage in case you find something you want to take with you while leaving your hands free. Add an Integrated Tool Set and you can cut that down to forty storage points.)
So from my perspective, this system looks nice, not because of what I can and can’t wear, but because it automatically drops things in the appropriate layer, and I won’t have to go through my advanced inventory every time I put on a pair of socks to make sure that I’m not wearing them over my boots. Even if that was all it did, and the encumbrance system was unchanged, I’d call it a major quality-of-life improvement for the game.
That being said: it seems to me that only the outermost layer of each category should grant storage, at most. Nobody loads up a set of cargo pants and then puts on a set of cargo pants over them. It wouldn’t fit, and even if it did, you’d have to take off your pants to get at your pockets. That’s not a problem with the new system specifically, though; it’s been around for as long as I remember.