Hide rare kanji readings is a setting that goes with don't use new system. I had to switch because I didn't want to get quizzes on 50 kanji with readings I haven't studied after the data correction. I'm now on no extra readings. It was more manageable with around only 10 kanji to be quizzed immediately, and now I am manually studying the other 40ish. The Hide rare kanji readings setting though is only available with don't use new system. Can it also be a setting with the other settings?
It would be quite difficult, off the top of my head, to layer two different types of reading filters on top of one another (especially as most of these are done at the sql level when filtering out terms for quizzing).