On Flow pages links to disambiguation pages does not use the class "mw-disambig"
Exception : when writing or editing a message as it uses VisualEditor classes and VisualEditor handles Extension:Disambiguator (or vice versa)
Example : https://test.wikipedia.org/wiki/Topic:Tdjd6kijr6fp4mb8
Checked in testwiki and betalabs - the links to disambig pages have
<a class="ve-ce-linkAnnotation ve-ce-mwInternalLinkAnnotation mw-disambig" href="https://test.wikipedia.org/wiki/Quechua" title="Quechua"><img class="ve-ce-nail ve-ce-nail-post-open">Quechua<img class="ve-ce-nail ve-ce-nail-pre-close"></a>
That's the link when you edit. Once saved it becomes :
<a href="/wiki/Quechua" title="Quechua" rel="mw:WikiLink" data-parsoid="...">Quechua</a>
We can probably fix this in the same place where we fix link paths and red links and stuff.
I agree, but like the red links, it should eventually be fixed in Parsoid: T149794: Mark disambiguation links in Parsoid.