`Manifest-Metadata-Consistency` not considering root nodes

[Trenly]

• New version: Fly-io.flyctl version 0.2.2 #138983

In the above PR, the Manifest-Metadata-Consistency label was applied for

=== manifests\f\Fly-io\flyctl\0.2.2 ===
Missing Properties value based on version 0.1.76:
NestedInstallerFiles

However, the commit did have NestedInstallerFiles, it was just placed at the root node instead of the installer node

[Trenly]

[Policy] Area Validation Pipelines
[Policy] Area Bots

[Trenly]

#139940