One, Luffy doesn't have better physical states than Zoro, not in base. The reason why Luffy looks like he has the better physical stats is that Zoro is not adept at channeling his powers via his limbs the same way Luffy's not adept at channeling his powers via weapons. At least, Zoro could punch better than Luffy could slash people.
Two, Luffy has a higher level of CoA than Zoro but it's not necessarily stronger. You could have a stronger level of Haki within the same level of CoA, and you could have a stronger Haki than those with more advanced Haki too. For instance, Gorgon sisters have the barrier variant before TS—It's an advanced form of Haki, but you can bet Luffy's CoA was stronger than theirs even before he achieved advanced forms of CoA. Similarly, Luffy's CoA is of a higher level than Zoro's because it's more advanced but Zoro's Haki is still more powerful. That's why Zoro was inflicting better damage despite Luffy having the ability to penetrate Kaido's defense.
The premise here is, that if two people of equal caliber attack the same thing/person while one is a swordsman and the other uses fists, then the sword attack is always more lethal. So if Luffy hits someone with X amount of physical power internal destruction Haki then he'd do less damage than Zoro using the same amount of physical strength and the same level of Haki.