I remember back when I was making kanji study materials for my classmates, I had a lot of trouble finding any useful vocab that used the じ reading.
That being said, I do think “semi-approving” it (or whatever you call it when the screen wiggles but doesn’t mark it as wrong) makes a lot of sense; it is a Jōyō reading, after all, so it seems a bit harsh to punish people for knowing it.