He just is, better physically, better defensive positioning and he’s a leader. Varane’s been lucky to play next to Ramos and he’s the clear second best CB in Madrid while Koulibaly carries Napoli’s defense by himself with average fullbacks, average goalkeeper and an average CB partner next to him.
Koulibaly is at an elite level, Van Dijk, Ramos, Pique and Chiellini are the only other defenders at the same level. Varane is a level below that.
That is if he goes back to his normal level, this year has been shocking for Varane.