Hi AliSafari,
Tested in 2019.3.6f1 and 2019.4.2f1 on windows but after test these issues on 2019.4.2f1 I realized that all my complains come from the fact that Substance Plugin is in Assets Store not a GIT repository that why there is not references in manifest.json and all files are stored in Assets folder.
So the only real issue is why I see version 2.4.5 as the latest version in the Package Manager windows but in the website is 2.5.1 but I doubt this can be solved in the side of substance team.
Regards