Project is about transhumanism ala Ghost in the Shell. Every champion in the line is completely human looking and a cyborg.
Program as a skin line has some "odd cases", champions with human features, but not completely human looking and they are complete robots. Examples for these cases are Nami, Lissandra (legs permanently covered in ice), Camille (who doesn't look completely human anymore because of her blade legs), and Soraka (space goat).
And Ivern is actually a plant... how many plant cyborgs do you know from any kind of media? It would be strange. However, if Ivern is a real robot, just designed around the idea of a tree man, then it can make sense in this future setting.
And like Sukishoo already pointed out, with the aesthetical design of Program they could reference Baymax from Big Hero 6. He definitely looks more like a Program design than a Project.