Marx is saying that both nature and labor are required to generate value and they can't exist independently of one another. You're not disagreeing with him, you're saying much of what he said in Capital.

Marx also cites rarity as another source of value distinct from labor, but rarity in terms of natural resources. And yeah you're right, rare natural resources typically correlate with specialized or intense labor, but not always.

There's some part of capital where he talks about pearls and diamonds specifically being an example of this natural material rarity stuff. You can randomly find pearls and they're highly valued, but most pearls are found through specialized labor. Nature created the pearls, humans procured them through labor, both inputs were necessary to create the subsequent value.