Oh, of course! I know you're always responsive to issues, and I'd never think you'd do anything intentional to upset users. That's why I've stuck around for so long and why I don't hesitate to open issues if I find them.
I was the one who brought up the 上げる/挙げる issue, using the "report mistake" function. And thanks for removing the "rarely written as kanji" from those. They, along with 揚げる, now show up with their proper kanji in schedules. That issue in itself highlights the problem with "rarely written" words. While it's true that you see あげる, you just as often see 上げる, especially in compound verbs. And 上げる and 挙げる, though they basically mean the same thing, can be used differently. It's important to be able to study all versions.
I know you're not the actual person deciding if something is rare or not. It's common across all the different Japanese dictionaries, but I personally take "rarely written as kanji" notations with a grain of salt. An example is 頃. It's always listed as rarely written in kanji, but in news articles and official statements it's part of the standard notation for time when the time is approximate: 4時20分頃. You see both ごろ/ころ and 頃, depending on what you're reading. Beginners might best start out studying the hiragana versions, but they'll run into the kanji version soon enough and may want to study it. As htatsuha suggested, a way to individually mark words to display with kanji or kana might be a solution to problems like this instead of an all or nothing setting. (As someone who's done software development, I know that, depending on how the program is set up, such a change might be simple to do, or it might require a complete rewrite of everything, so I understand any hesitation you might have on that.)
As I go through my schedules, I'll collect words that I think you could unmark and post them. Thanks!