Because on average, Xebec's Haki was stronger. But that doesn't really matter since, when they but the entire weight of their Haki into their attack, their Haki overpowered his.
Unless you are saying scars only magically appear if on average Roger's Haki was stronger than Xebec's. Which doesn't really make sense and is an arbitrary rule made up. Damaging and scarring Kaido's body follows fundamentally different rules than damaging DR people. Unless you say that if Roger and Garp tore Kaido to pieces with their attack, he would've reassembled due to having stronger Haki.