As someone who thinks that the current loot system is as bland as it gets AND wants slow, meaningful, progression:
Gathering higher tier stuff, no matter if you can't use them effectively yet, is a bad idea. Not when you can just stroll through a SM or find almost any POI anywhere on day 1, not when those so-called "sealed crates" are everywhere. The less prudently items are distributed into the world, the more any sense of exploration, looting, crafting etc are trivialized as the game progresses. Not that it particularly matters without an item sink but anyway.
So the devs are like "ahh, yes, we have vertical progression in the game, let's achieve that by handling the distribution of items with a meta number, that guarantees the same results in every playthrough, is known by the player at all times, renders unique POIs and containers rather meaningless in early game and, in general, makes the spatial variety we have worked so hard to create obsolete". Which is nothing new really, but became painfully obvious, gameplay-wise, with the latest change.
No wonder someone gets disgruntled when they visit that SM, open a sealed crate and find that stone axe on day 1, *rightfully* complain, and then have others *rightfully* tell them "what did you expect on day 1". Ironically, both make a valid point. Thing is, what players visit throughout their playthrough hardly changes, ergo what they visit doesn't matter much. It's that meta number that matters - almost solely. Which is why what @stample said, is among the excruciatingly few good concepts in this thread.
1) Remove type-specific (Shotgun Messiah, Working Stiff, etc) crates from all T1 and T2 POIs, except thematic ones (T2 Working Stiff, for example)
Not that this alone would change something for the better but it would be a ...start.
And biome modifiers will help, sure, but the thing is, that's just what they are - modifiers - they are not meant to *gate*, and even though they will offer some nice difficulty variations between areas, if they keep scaling perfectly with the player's level at all times, I don't expect they will really bring any meaningful variation to the players' visiting habits. Which is why I roll my eyes every time I hear someone saying "the latest change was a necessary step towards the system" etc etc.