Ah, sorry. I will write more simply, then:
Verbs like 診る and 観る are clearly derived from the same concept (looking at something), but the kanji helps to differentiate between them. Probably, they were the same word in ancient days, so the kanji distinction was added later, to make written language more obvious.
But many unrelated words have the same pronunciation as others, like the DOKU example I gave. "Single" and "Poison" don't have any connection in meaning, but maybe, just like all the different MIRU, some people might think the words have a relationship.
And maybe there IS a relationship between words like that, but it's obscure and we don't know about it.
I was just wondering if a native Japanese speaker also does this kind of "毒心" connections when they learn new vocabulary growing up.