M13 Goku was stronger than Ultimate Gohan and SSJ3 Gotenks by a large amount if I'm remembering correctly. I'm not sure if we have reason to believe that Trunks would have reached that level by the Baby arc, at least in Base. If Trunks is able to transform I think he'd win.
Goku stomps considering even his SS2 self was treat as superior to Ultimate Gohan. Even with SSJ, I'd say Trunks' feats only place him above Base Rild, so he'd probably lose even if it's allowed.