Currently source-build build injects a PackageVersions.props into the repos builds that contains the current source-built package versions as well as all previously source built package versions. The result of this is that source-build does not behave the same as repo builds. Often times repos define Versions.props entries that are not auto-updated. They do not have a corresponding dependency in the Version.Details.xml file. Yet the way source-build works, these Versions.props entries are getting updated to use the source-built versions.
The solution to this is to build up a repo specific PackageVersions.props based on the dependencies defined in the Version.Details.xml. This will get source-build to build like the microsoft build and will be a forcing function to ensure the appropriate dependencies are defined (in order to eliminate pre-builts).