The convention-based build will auto-increment the version number. A custom build script (examples at http://docs.myget.org/docs/reference/custom-build-scripts) can override this behaviour and use a tool like GitVersion or something similar to set the version number. A custom build script would also let you specify the version number manually.
However, there are a couple of downsides to manually setting the version in source control. It becomes important to increment the number on every commit, as each build would otherwise produce a package with the same version. Which in turn means that a consumer of the package will never get a new version, as the local NuGet cache will not update the package binary on their system. The same applies with our CDN, which has similar caching mechanics.