I don't think Old Kaioshin was factoring in hypothetical Fusions when he made that statement, so Gotenks-Boo stomps. If we assume that Gohan was the other master, then a Fusion of Goku and Gohan would still qualify as a Fusion of "two of the top 3 masters in both the living world and afterlife" and also be among the strongest anyway.
I don't think their rivalry really contributed too much to the Fusion, either. To me it just sounds like he's saying their rivalry is always pushing them to get stronger, which would obviously make Vegetto more powerful since stronger components = stronger Fusion.