I honestly wish it was Jonathan that beat the big bad Heaven Dio. Since they have the same body, the weird Valentine law would apply. Have Jonathan just bearhug him, sorta like how he holds onto Dios head at the end of PB. He holds onto him and they both explode. Big heroic sacrifice for Jonathan, less Jotaro wank, less of a lazy rehash of Part 3. I dunno, seems more fitting for a game featuring the entire lineage.
to give you the long answer. It wouldn’t work. The bodies are too different.
Sometimes people forget that Dio’s body changed after 100 years in the coffin. It’s why Araki draws SDC Dio differently than Jonathan and why in canon you never see that fanart thing where people draw the body so it doesn’t match the head. If Araki’d wanted it any other way, he’d have spelled it out. But Araki doesn’t think of Dio as unchanging, it’s the opposite: he defines Dio by physical change (one of the reasons I like Dio tbh). Araki’s vampires are super healers and it’s spelled out that they quickly replace any host cells with their own (even if Dio’s healing’s not at full strength the way he claims, it’s still pretty top-tier, we see him quickly reattach his entire leg). So think of Jonathan’s body like an old house that’s been gutted and entirely renovated to suit the present owner.
There’s probably some traces left in DIO that bond him to the Joestar bloodline and the Joestars back to him, but DIO’s no more the same as Jonathan than a distant cousin.
Take it one step further because Heaven Dio hasn’t just transcended humanity once, he transcended a 2nd time to become a God. Heaven Dio’s body isn’t even the same as Pt.3 Dio. He’s purple fgs.
Jonathan definitely got shorted in story mode, but if Jonathan hugged Heaven Dio, you wouldn’t have an explosion you’d just have both of them looking really confused.