Currently the generated <map-link rel="query" tref="https://mapserver.example.org/wms_cgi?request=GetFeatureInfo&...&info_format=text/plain"> is fully directed by default at the remote WMS, using the info_format=text/plain GetFeatureInfo parameter by default, since it's unlikely that the remote WMS supports text/mapml yet.
There should be a way to obtain the MapML response containing a <map-link rel="query" tref="https://my-geoserver.example.net/geoserver/.../?request=GetFeatureInfo&info_format=text/mapml...">
This could be done via a checkbox in the MapML layer Publishing panel, and it could be represented dynamically via a format_options mapml query link control parameter (name tbd).