To be fair, it's not just a Jonathan problem; it's a Stranger Things problem. If they're not casting the part of a preteen, they have no idea what youth looks like. During the new season, the first time I saw Billy speed into the school parking lot in that dope muscle car, I was pretty sure he was the hot, new janitor.
Heaton says he won the Duffers' attention during a Skype call at a burger restaurant. So I'm thinking that if it was late at night in a burger joint with good fluorescent lighting, sure, he passes for 16. Much in the same way I pass for someone who hasn't just eaten three cheeseburgers.
As for the role of Billy, the only explanation I can fathom is that Carmen Cuba is the casting director for Stranger Things, and she also cast all of the abs in Magic Mike. Don't you dare ever say a word against her. She has brought more joy into this world than you can possibly fathom. But it makes sense when you see Dacre Montgomery like this: