A file is generated using some common ideas about which files should be included in the source distribution. If it does not exist, it can be easily restored. Typically, if you want to make changes (for example, by adding a file that the generation does not use by default), you actually make changes to the MANIFEST.in file . The Manifest.in file that MUST have a version with is version controlled.
Of course, in some cases, you may need to create the MANIFEST file yourself and not rely on auto-generation at all. In these cases, you will need to control the manifest file versions.
I did not face any need for version control, but you can leave the question open for other comments, since I also do not have much experience in developing a more complex package.