For papers sponsored by WMF that don't have a WMF researcher in the by-line, there should be some formal recognition of WMFs support included in the acknowledgements section. Similar to "This research was supported by NSF grant number 1039r020".
Since we don't have a numeric catalog system for formal collaborations, the message could be as simple as "This research was supported by the Wikimedia Foundation", or it could have a link to research.wikimedia.org as well.