TOML is a better format for configuration files IMO, if not for many reasons, primarily because TOML accepts comments.
However, one annoying thing for TOML was the lack of schema, and the reliance on JSON Schema for that. Which I decided to tackle years ago when I started the TOML Schema project. In the past few months I leveraged code agents to take to the finish line and got something compelling: tomlschema.org
Interesting. The website says that it's "validation-focused". I don't know how that plays out for TOML, but the lack of focus in json schema to define an interface in addition to validation can be very frustrating. Most of the time I would rather trade off some expressitivity in terms of validation in favor of having a defined typed interface into the validated data.
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.
However, one annoying thing for TOML was the lack of schema, and the reliance on JSON Schema for that. Which I decided to tackle years ago when I started the TOML Schema project. In the past few months I leveraged code agents to take to the finish line and got something compelling: tomlschema.org