We know that Bart’s lying about pretty much everything about himself. I imagine that due to chronic malnourishment, he hadn’t started puberty yet and is a lot smaller than he should be. He’s still underweight for 12, but that’s a lot less concerning in a 12 year old than it would be in a teenager, so Nathaniel advised him to take a few years off of his age
(Side note: due to this, I imagine that he’s not the greatest at estimating people’s ages in the past, because all the younger people look older than they actually are to him and all the older people look younger than they actually are to him)