Does setuptools support replacing the Manifest.in file, which specifies files that should only be included in the sdist distribution with a declaration in pyproject.toml?
Setuptools does not currently support replacing the MANIFEST.in with a declaration in pyproject.toml.
There is also currently no specification for how to control the files included in an sdist.
There are other build backends which do support this, by using their own tool subsection of pyproject.toml. For example, hatch uses [tool.hatch.build.targets.sdist] to control the sdist content, see File selection for more details about that.