For Five Yen!

Yato, because he’s a good person/was learning how to be from Hiyori and Yukine at the time, uses the same line to empower Bishamon. But we all know in reality gods can’t do whatever they want if they want to uphold the standards/way of life determined by their shinki, especially their guideposts. Yato following the “gods can do whatever they want” was essentially why for the longest time he couldn’t keep a shinki. They all had no faith in him specifically because he kind of really had no morals and in Yukine’s case (and potentially past shinki we don’t know about) that lead to stinging. What shinki wouldn’t act out when their god doesn’t lead by example? Mayu asked to leave but I think it’s safe to say not every shinki would even know they have that option at first. 

So, my epiphany was that Father telling “gods can do whatever they want” is an excuse to let go of Yato as soon as it’s convenient to him. 

We know Father hates gods to his core. He essentially uses similar wording to the phrase he tells Yato as to exactly why he hates gods in the first place. Humans pray and pray and pray to the gods but in the end, gods only do as they want. 

Even if Yato had never stepped out of line with Father’s wishes, it would make sense to me for Father to still turn around and say “you gods do whatever you want and so you can’t be trusted” as soon as he gained whatever he wanted from Yato [killing Amaterasu, literally all of heaven, or whatever it may be that he ultimately hopes to achieve]