The cluster of wikis in the deployment-prep project (<https://meta.wikimedia.beta.wmflabs.org/wiki/Special:SiteMatrix>) used to have special logos set which complied with the Cloud Services TOU [[https://wikitech.wikimedia.org/wiki/Wikitech:Cloud_Services_Terms_of_use#What_uses_of_Cloud_Services_do_we_not_like?|prohibition on using Wikimedia Logos]]. I noticed recently that there has been some regression here with at least the metawiki work-alike using what appears to be an official logo (although the Foundation logo rather than the meta logo.
On https://en.wikipedia.beta.wmflabs.org/wiki/Main_Page?useskin=vector there is an overlay added via a css rule that labels the wiki as being part of the beta cluster, but https://en.wikipedia.beta.wmflabs.org/wiki/Main_Page?useskin=timeless has no such fix.
This all seems a likely side effect of changes which have been happening in the skin layer of MediaWiki and configuration drift.