Those stampeding mares in C&D are the Toon actors who played the characters on the show. That just means the G4 humanoid Toon actors are also short, and the production team scaled the sets to fit them.
There’s also no evidence the G1 and G4 ponies’ actors were the same size. The realistic human Toons Megan, Danny, and that king were probably human-sized like Jessica Rabbit or Cruella DeVille, while the Equestria Girls have the proportions of a Betty Boop. I’d expect Capper’s actor’s height to be roughly that of Daffy Duck.