system
A chat on subreddit /r/NoStupidQuestions
human
The two words come from different origins. Human comes from Latin, man comes from Germanic.

Maybe it's not a coincidence that we ended up spelling them so similarly, but the original similarity is a coincidence.
gpt
Exactly, you only have to take a look at latin based languages to see it. T.ex Spanish human=humano man=hombre. 
Meanwhile in German based languages like Swedish we have Human=Människa Man=Man 

English simply took one word from Latin and one word from a Germanic language and it was pure coincidence that man was used in both cases.