Python packaging is a bit of a mess already, so when I recently started a new small package I wanted to choose tooling that would not clutter, but a fair amount of tool makers were reluctant to allow code into their repo that would use the unified toml rather than a ton of separate file.
.config is probably a better solution than a single top level toml, IMHO, but far more important is doing something unified rather than continuing the pollution of the top-level namespace, which merely obscures the project structure.