To fix this we either need T97093: Parsoid should mark interwiki links as such to be fixed in Parsoid, or do a reverse interwiki map ourselves.
This also causes [[:en:WP:Flow#Design FAQ]] -> https://en.wikipedia.org/wiki/Wikipedia:Flow#Design%20FAQ meaing that section links with spaces in them breaks. This is a huge...no-no.
This looks to be resolved by the Parsoid changes. For example, on https://www.mediawiki.org/wiki/Topic:Uy2zmj89ja68cget, the link phab:T165162 renders correctly: