Funnily enough, the author of the Shinza series addresses this kind of thing in one of the interviews
Q: As far as I understand, Yato is the strongest hegemony god in history besides Hajun, but he only got Yatsukahagi for his legion (souls). I assume he was completely alone by the time he fought Habaki, so is he really still stronger than the Mercury was in Dies?
A: Sure is. As I mentioned already, a hegemony god’s strength depends on their craving’s strength as well as the quality and quantity of their legion. This means Yato surpasses all the hegemony gods in history by craving alone. It’s pretty much unfair, to the point he kept fighting against Hajun for thousands of years. If it somehow wasn’t clear enough in his fight with Habaki, let’s look at this from another point of view. Yato had no reason to destroy the world, so he didn’t use any cosmic-scale attacks in his fight. That being said, it’s not like he tried to go easy on Habaki: it’s simply a matter of quality. Basically, the scale and the depth of the offense are two completely different things. If we imagine a pebble that can’t be destroyed even by a nuclear blast, cutting it in two with a sword would mean that the sword is stronger than the blast. All the different techniques Yato used that time were more like swords. Something like that.