Tying the loot to game stage just removes the desire to visit any difficult POIs or crack any safes because I'm just going to get stone axes anyway. It's bad enough that zombie difficulty is tied to loot stage. They too should be tougher in tough POIs. Give me a reason to go out there.
1. Higher quality stone tools/weapons are very valuable to those who do not have the skills to craft them yet. My pure agility run was very happy to get higher levels of stone axe and shovel. I don't just have a desire to scavenge and hit those safes, they give me important upgrades as well as....
2. Tools/guns =/= all of progression, it's a tiny tiny slice of overall progression. Books, recipes, schematics, dukes, cobblestones, cement, stone, wood, paper, brass, lead, iron, etc. POIs provide all these things and if you don't have miner69er and motherload and you don't have recipes then POIs offer amazing progression.
3. If you decide to take every single "I'll mine it and craft it myself" skill then you've chosen to focus on self reliance instead of scavenging and so the rewards won't be as great for you because of your own choices. Concentrate on playing how you skilled yourself to play. Farm resources, use that trader, and craft your own stuff. Hit the occasional POI when you feel like it but it's supplemental for someone taking those kind of skills. Remember, this isn't A16 and before anymore...you have to make choices about what you are good at and what playstyle you want to have. Everything is a tradeoff.
4. Tying loot to gamestage is tying risk to reward. I don't see a problem with that.
5. There IS a problem with not being able to use your ranged specialization early. TFP is working on it. They have ideas about adding in additional weapons like pipe guns so that there are more T1 ranged weapons. For now the blunderbuss and the primitive bow cover early game ranged weapons until proper firearms but they are definitely looking to improve that.
6. TFP has direct plans to give custom gamestage modifiers to specific POIs. The tech isn't in yet though. The plan is to have something like Shotgun Messaigh be considered a much higher gamestage. That way you can get that better loot early, but you'll face much tougher enemies to do so. It's planned to be risk vs reward.