Leaving users having to guess where in the hierarchy you decided to hide something, that they know they’re looking for doesn’t add value. No, just keep it flat and simple.
Yes, "toml" would be perfect, but we're getting "tomllib" instead, due to the lack of namespacing that the parent comment is lamenting.
The problem with the current situation is that (1) every project has to keep all the standard library modules in mind and make sure to never name a module "io", "site" or "email", etc. and (2) once a non-conflicting name has been picked (e.g. "toml") it will break if the standard library later introduces a module with the same name.
(I'm not advocating for Java's endless chain of single-child directories though.)
Who knows, it could be a good feature to earn the 4.0 moniker.