No, I don't think they are. For example, a credit card processing fee doesn't raise the price of a gallon of gasoline.
There is supposed to be a difference between markup and a fee. We don't have to hash out what exactly the difference is, just observe that there is a difference.
It's a common grift to hide part of the price in unadvertised "fees" so that consumers will have a harder time comparing options but it is just that, a grift. It's deception.