I just found a kind of pattern and I’m curious to see if there are more examples of this.
So, 元 means “origin” and its Kunyomi reading is もと.
本 can also mean “origin” and its Kunyomi reading is also もと.
Same way, 円 can mean “circle” and its Kunyomi reading is まる.
丸 also means “circle” and its Kunyomi reading is まる.
Also, is there a reason as to why only the Kunyomi readings are same in these cases?
This is more a failing of one word English glosses than that they actually mean the same thing.
元 as origin is like “starting point” while 本 as origin is more like “foundation” or “root.”
円 is used for flat, disc-shaped things. 丸 is used for spherical things.
This happens when you get a one-word English gloss that is broader than the kanji meanings. You can usually find monolingual expalantions for these kinds of things by doing a search like 円 丸 違い once your level of Japanese is high enough.
This is natural, since the kunyomi is the Japanese origin word, and since there is overlap the same word got applied to mulitple kanji. The onyomi readings come from Chinese where there was a more fine grained distinction.
It’s basically the same thing you noticed happening with the English overlap but happening with Japanese overlap.
i do think there might also be some etymological shenanigans going on. my guess is that it was a case of a japanese word being mapped on to two chinese words: e.g. なおす might have meant both to fix and to heal (直す/治す), those are similar concepts after all. then the chinese came along with their fancy writing system, which used different words for fixing things and healing people. and as you start writing things using these shiny new characters, you adopt that difference in writing, even though you still think of it as the same word.
and several centuries later you’ve got language learners going “why do these words sound the same, even though they are written differently?”
this is pure speculation on my part, so please do let me know if i’m wrong 
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