Some extensions (WikiLambda, Wikibase) use the HtmlPageLinkRendererEnd extension to customize links on a page.
This is related to the Semantic MediaWiki behavior in T76278: Parsoid renders "invisible" SemanticWiki links except SMW used the InternalParserBeforeLinks hook to do this.
Regardless, Parsoid doesn't use LinkRenderer for article link text, and so these transformations are expected to be unsupported in Parsoid Read Views.
@JoelyRooke-WMDE just FYI this falls into the category of functionalities Parsoid won't support that might affect Wikidata integrations in the future, this is just a tracking tasks for us to hold the discussions.
https://codesearch.wmcloud.org/deployed/?q=HtmlPageLinkRendererEnd - the only WMF-deployed extensions using this hook are Wikibase, EntitySchema, and WikiLambda.
WikiLambda assures me their use is only on Special pages, and they would welcome a new narrow hook to do that they need to do there.