What is difference between Github Project and Git from Source Code Management?

Github is dedicated to using github services and it unlocks specific github features.

The other will work with any git SCM server including external vendors (github, bitbucket, your own infrastructure , team foundations server etc) . This means it will support only git standard features, nothing that is vendor specific.

You can configure both without problem.

If you install bitbucket plugin, you will have a similar third section.