With nature Marx means the discourse at that time, which was based on Ricardo and a specific conception of Nature. In that nature means less gold in the ground, but the world we live in, the materiality of it and with it the ecological interconnectedness of it. "Nature" gives us apple trees and makes apples from them without human labour, but an apple eternally on a tree doesn't feed you, only labour does make it useful. Marx (and Says, Ricardo, Smith, Korpotkin etc.) do agree that there is wealth to be found in nature, that can be exploited alas only with human labour.

Of course there are edge cases like a breathable atmosphere. That however is currently not something with exchange value (only indireclty via tourism)

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.

from volume 1 of capital, which might give a better idea of what marx means. i dont think youre actually disagreeing.

The use values, coat, linen, &c., i.e., the bodies of commodities, are combinations of two elements – matter and labour. If we take away the useful labour expended upon them, a material substratum is always left, which is furnished by Nature without the help of man. The latter can work only as Nature does, that is by changing the form of matter. Nay more, in this work of changing the form he is constantly helped by natural forces. We see, then, that labour is not the only source of material wealth, of use values produced by labour. As William Petty puts it, labour is its father and the earth its mother.