While definition of the python package and other functionality using setup.cfg is perfectly fine, is becoming the legacy approach in favour of pyproject.toml.
While MUSE has some information in pyproject.toml, it is mostly empty and all the information is still in setup.cfg. This should change. A guide of what a pyproject.toml file should look like with all the relevant sections can be found in the setuptools documentation.
Note that there are other tools using setup.cfg that should be moved, and others that cannot be moved because they don't know how to use pyproject.toml yet (e.g. flake8, which should be moved to its own .flake8 file).