The current conversion only takes into account plain text tags and ignore everything else (in the case of this a link for example, the content of the ref is identified as link tag and so is ignored). It's actually the same for everything that end as XWiki macros, actually (in this specific case the macro is {{footnote}}).
The good news is that the bliki parser seems to properly parse the content of the reference. So the fix would involve doing something similar to what was done in the Confluence importer: allow indicating a target syntax so that we can do a conversion from tags to the indicated target syntax to produce the macro content (which can only be a String in the XWiki model right now). In terms of code it means everything which manipulate https://github.com/xwiki-contrib/confluence/blob/confluence-9.94.0/confluence-syntax-xhtml/src/main/java/org/xwiki/contrib/confluence/parser/xhtml/ConfluenceXHTMLInputProperties.java#L97-L110.
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