If the devs' idea is to fashion a thrilling ride through the POI with a big payoff at the end - which it seems they definitely want to continue to do - then I dunno if we'll ever be rid of "loot rooms". Or, at best, there might be a couple/few loot rooms all at the top level of the POI to ensure you enjoy the ride first. Doesn't work so well in T1/T2 POIs.
Also I expect that whatever change is made will depend on the resources required to implement it. I think that redoing most of the POIs to add appropriate loot rooms with appropriate One True Paths to them could be a lot more work than (programatically) replacing metal_loot_box_01 (or whatever it is) with keyed_metal_loot_box_01 and likewise for other Big Loot Containers.
Placing the key within the POI will require some changes to the code which generates (or resets for a quest) the POI, but I think they might be able to (also programmatically, not by hand) adjust loot tables so that the key can appear in the existing lootables. That is, the wouldn't have to go touch every POI by hand and place several "key container" objects around. They might just be able to adjust the loot for dressers, desks, kitchen cabinets, and whatnot to have a possibility of producing that POI's key.
Anywho, avoiding having to touch all the POIs by hand is probably a factor.
Personally I think I prefer just spreading it around more. The key idea is going to just introduce more indestructible elements which I am very much against and/or invalidate lockpicking tools which would be dumb.
That would be dumb. But how about this:
1) One Big Loot Container in the loot room is
almost indestructible (say, 50,000 HP)
2) If the BLC is destroyed, either by smashing or by falling, its contents are lost - so you can remodel the loot room if you're making a base, but ixnay on breaking it for loot
3) Lockpicking still applies to BLC, but perhaps it requires perk level 2 or 3 to use it on them.
I think all of those rules would be easier to implement than a redesign of most POIs to incorporate multiple loot rooms. There's too much One True Path going on in them and it'd have to be reworked so the loot rooms were at least something of a challenge to get to.