I'd argue that for code, yes, JSON is vastly closer to computer structures.
I think this is the real "why do so many tools have JSON config files": because it's just a literal notation, for basic data structures, that looks a lot like what many programming languages natively do, what their data structures natively are. The answer to the post is: it's mechanistic sympathy.
For humans, I do find TOML to be a lot easier to manage. Even if you have a really good editor that takes care of all the quoting/nesting/comma concerns for you, even if you have jsonc or json5 with comments, it's still not as easy/friendly as a big flat file with sections in it.