I dont really agree with that reading at all. Phoenix was prepping Apollo, but really cases 2 and 3 have little to do with the main story and I dont think Phoenix ever really thought
Apollo would betray him for Kristoph or anything like that
Phoenix straight up admits in the fifth game that he disliked Apollo at first and that it took him a while to change his mind. I don't remember his exact wording. We don't know why Phoenix chose to recruit him, but it wasn't because he had an instant liking to him. I believe it was a test to see how Apollo would react.