Im gonna be honest bro, having upgrades to make the breaking easier and then just making the blocks harder to kill feels incredibly unrewarding.
Don't get me wrong I love the idea and most of what you've done, but the way you're scaling the difficulty makes it feel like there's no difference between bronze and diamond pickaxe power, just more effect on screen. You roughly destroy the same amount of blocks.
Increased max bonus from boxes is semi-useless as well. With the difficulty scaling you're lucky if you can get 5 upgrades per type in a run.
I'd make the price scaling for skill tree upgrades go way up and then the unlocking of new resources just adds a multiplier to all resources below it. So like you unlock gold and iron/bronze/silver each get a X2 multiplier, while the rocks get like a X5 hp multiplier. (estimates, would require testing of course)
This way you're giving the player a choice of when to upscale difficulty and you also get a better feeling of incrementation of power since before an upgrade a run would go for a lot longer. This way there will be a clear feeling of increased power beyond just slightly bigger numbers.