Currently CustomOrganizationFolderDescriptor only works if the plugins offering SCMNavigatorDescriptor (like github-branch-source) and MultiBranchProjectFactoryDescriptor (like workflow-multibranch), as well as branch-api itself, are already loaded during Jenkins startup.
Basically this code would need to also be run in response to an ExtensionListListener, though that requires a 1.625+ dep.
Alternately, we could fix the problem the right way in DescriptorVisibilityFilter, using a new core API dependency.
Whether it is fixable using the current 1.609.x core dependency, I am not sure. HideGeneric.filter is called every time the New Item page is displayed, but it is probably too late to add a descriptor to the list while that list is being filtered.