One unknown issue (that works with setuptools specifies data/share/swig subfolder in setup.py but not in pyproject.toml) is whether or not those swig support files that get installed will be included in the correct subfolder when building using scikit-build-core.
Try migrating from scikit-build to scikit-build-core, which could remove the need for setup.py and MANIFEST.in files.
https://github.com/scikit-build/scikit-build-core/issues/274#issuecomment-1508493949 mentions an additional step that is needed for using setuptools_scm for versioning.
One unknown issue (that works with setuptools specifies data/share/swig subfolder in setup.py but not in pyproject.toml) is whether or not those swig support files that get installed will be included in the correct subfolder when building using scikit-build-core.