Another thing that comes to mind are the Rahkshi as "sons of Makuta".
I dimly remember some answer regarding this choice of words - could have been Greg, but I'm not sure. Basically this would only be the "English translation" of the language the people would speak in-universe. So "mother" in this context could just mean "creator" whereas "son" translates to something like "coming from/created by".
It is reasonable for a Matoran to assume that someone must have created Rahi, even if he doesn't know who. After all Matoran legend has it that the Matoran themselves were created a long time ago.