Compare https://www.mediawiki.org/w/api.php?action=query&list=usercontribs&ucuser=Mattflaschen%20%28WMF%29 to https://www.mediawiki.org/wiki/Special:Contributions/Mattflaschen_%28WMF%29 . See https://www.mediawiki.org/wiki/API:Usercontribs (User contributions API).
ApiQueryUserContributions does its own DB lookups, using the ApiQueryBase infrastructure.
It doesn't call any hooks directly, which is probably why it's not picking up our ContribsPager::reallyDoQuery listener.
This looks like it will either require adding new hooks, or refactoring ApiQueryUserContributions to share code with Special:Contributions.