Thanks for clarifying. I can certainly appreciate the reasoning behind the change. I have a few points of feedback on the change.
First, there are cases where the readings are identical, except for a dash. For example, today I reviewed 「天」, which has readings of both 「あま」 and 「あま-」 listed. However, it's not easy to remember when a kanji has a dash form of a reading listed, and I feel that there isn't any benefit to the learner of having to type out both, when a simple 「あま」 would show that he's learned the reading.
Also, similar to the first point, there are several readings where one reading is simply a copy of the other with diacritics (either dakuten or handakuten). I came across this today as well in reviewing 「板」, which has as onyomi readings both 「ハン」 and 「バン」。 I recognize that at a beginner level, this may not be intuitive, but for everyday usage, this becomes a fairly easily deduced reading.
Finally, should obscure readings be marked as known by adding one or two rare vocabulary terms, it forces the learner to either go back to the kanji and turn it off, or else spend his study time reviewing a little-known reading simply because he wanted to learn a specific word. (If this is not how readings get automatically marked as known, please disregard.)
I'm not sure whether or not the third point bears any attention, but for the first two, I would like the ability to only have to type in one reading in these instances.