There are several differences. Off the top of my head, z’man Mincha and Maariv, bein hashmoshos for certain situations (e.g. amirah l’akum l’tzorech), mayim shelanu.
Mind expanding a bit? Remember, they would also hold of the Gaon L’Chumrah (Assuming not as a minhag, but a real safek, like the MB).