Yeah certain readings are prioritized. I don’t think WK ever teaches かみ for 上 or しも for 下 either. It usually prioritizes the most common ones and is content to leave out competitively rarer uses, particularly for kanji that already have a lot of readings.
That was the humbling part for me… I thought the first Iknow lessons would be a breeze since I already learned so much in WK… and in lesson one came all these 上 and 下 variations 
There are a few cases where WK will allow multiple readings. You can answer 私 with わたし or わたくし, and 品 with ひん or しな, for instance. Other times, there are valid readings for a vocabulary word, but WK won’t accept it. 空 is only そら, not から, and the 止める example you found. 角 manages to fall into both categories, since WK will accept either かく or かど but not つの.
Trust the Crabigator, learn what WK teaches you, and be aware you may run into homographs for some of the words that WK didn’t cover.