As you can see the おじ I am quizzing on doesn't appear in the dictionary, has a slightly different meaning, both have different images and both show up during my srs.
It is like if the one I'm quizzing on, instead of being merged it was just only removed from the dictionary.
It seems this dictionary entry was merged with the one that is visible when searching for おじ as alternate reading. When searching directly for "parent's younger brother" the one you have in the quiz is found [has 叔父 as rarely written kanji], while searching for おじ results in 伯父 being shown, with 叔父 as alternate.
as you pointed out, they do have different definitions, which is linked to their Kanjis. No idea though why it is thrown together in one instance but can still be found separately in the other.
Just searching for "uncle" also only finds the 伯父 with 叔父 as alternate result. The image for 叔父 also shows up in the "uncle" search results, but is here used for 伯父さん.
I guess this would be better if there was an option such as "Show kanji for common hiragana terms" but that we could activate at the single vocab level, so I could turn it on for those two and get 伯父 and 叔父 respectively during quiz, definetly would be a more useful review session compared to おじ and おじ hehe :)
- That btw would also be a useful feature for people who have many terms studied (5k in my case), if they where to use the current "Show kanji for common hiragana terms" there would be so many vocab changing and without being first shown once in the review preview, that it would kill the SRS accuracy overall (and possibly even the will to do SRS after a hit like that :S).
They have to be transitioned manually and one at the time by the user for best resoults, I think