"best" means - with every attribute of the fighter combined - speed, strength, endurance, grappling skill, striking skill, defensive skill, heart, etc., who has the highest stats if they were video game characters. This is a much more speculative category than GOAT, "greatest", because GOAT is argued by accomplishments pretty much exclusively. Accomplishments factor into the "best" conversation, but there's more to it.
Stipe only beat Francis by taking advantage of his green grappling skills in the first fight. Once Francis removed that hole in his skill set (which increased his "stats"), Francis thunderously destroyed Stipe. So we clearly see that with both men at their best, Francis was much better. You can make a similar argument for Stipe in the Struve fight - Stipe may not have been at his best in that fight. Ok, fair. But he definitely was in the Ngannou rematch. Prime Francis is a better heavyweight MMA fighter than prime Stipe. You can argue Stipe is "greater", but personally I'm not impressed by 3 title defenses in the GOAT conversation. I think UFC heavyweight GOAT is ripe for the taking and really has not had a strong contender for that title. The field right now is particularly weak too aside from a few guys. The first guy to have 5+ UFC heavyweight title defenses is going to silence the conversation. And that guy will have a strong argument for "best" UFC heavyweight as well.