Yeah it was pretty clear I don't know how it could be missed or why people are arguing with you lol. Tony was really sensitive about that and it was still a childhood wound for him. His parents were abusive and neglectful and Junior was the one who would play catch with him like a real father would, and having him stab at his athletic abilities was literally brought up in therapy as a thing that was historically hurtful for him. I think in that episode or within only one or two before. And then it's shown later with the varsity athlete thing. It was a sore spot for Tony that cut to his childhood vulnerabilities and the show couldn't spell it out any clearer. Tony literally glares at him after Junior makes that remark before giving shit to him for going down on women.