“All animals are equal, but some animals are more equal than others.”
The initial reference refers to all animals without distinction. The second phrase differentiates, highlights, and refers to the "some"..... those with higher status.... the pigs and their totalitarian regime.
“The creatures outside looked from pig to man, and from man to pig, and from pig to man again; but already it was impossible to say which was which.”
The distinction between the pigs and the humans has completely blurred.... the pigs and human oppressors are one and the same.