FWIW, Pinyin is back on the popup, so it’s no longer necessary to save it with the translation (except of course where there are several pronunciations and you disagree with LingQ‘s suggestion). But yes, transcriptions (or, actually, traditional characters) above the text seem permanently disabled for ”known” words.
I think I get the idea: if the transcription is a learning aid, it makes sense to turn it off once the word is learned. But there are so many preferred use cases on LingQ that I do wish it could be customizable… (I personally don’t want pinyin above the main text, as I find it distracts me from focusing on the Chinese characters. But I do like to display traditional characters as a way to familiarize myself with them, and I do wish I could have them displayed on known words, too!)