Hmm, I looked into the law, and you seem to be right. Not sure now why the law was treated as the end of ‘independent’ Yandex News back then—though of course it was obvious that the gov wanted to control it and did everything it could think of, to that end. Personally I stopped paying attention to YN after that.

Rukipedia even has a section on incidents suggesting both manual fiddling with the YN output and the government's stuffing of it: https://ru.wikipedia.org/wiki/Яндекс.Новости#Критика

As for the example you cite: if it was found just in the ‘news search’, then it's possibly not from a source ‘certified’ for appearing in the main news feed—from what I've read, it seems that the search includes many more sources than the feed, and is possibly not regulated by that law.