Well, TOML is essentially just an extension of the INI format (which helped its adoption quite a bit, since you could just fork INI parsers for all kinds of programming languages).

And then, yeah, flattening everything is kind of baked into INI, where it arguably made more sense.
Although, I do also feel like non-techies fare better with flat files, since they don't have to understand where into the structure they have to insert the value. They just need find the right "heading" to put the line under, which is something they're familiar with.