I think where he's drawing the idea of Quarians on Rannoch from is from one of my favorite sequences in Mass Effect 3 during which they reveal some of the Geth's perspective on history, most of which has been lost or sanitized by the Quarians including the fact that there were Geth sympathizers during the Morning War who fought to protect their Geth friends/servants. I assume the ME fan fiction sub-genre he's referring to relies on the premise that some of them survived.