I totally feel you in terms of keeping things simple. How about this: MC and the kid don’t parent in a vacuum so the kid does encounter other families that would be considered nuclear (best friend has two parents mentioned during one of the parties.) So it would feel unnatural that the child doesn’t point out this discrepancy.
A few lines in the beginning about how other parent may have died or left during infancy and then maybe a mention of it as they are growing up would probably add to the realism. Not to mention give a reason why the story is the way it is.
Also, kudos on the sister scenario. I would like to encounter them again.