If Walburg and Gibson can't get a religious story right (Stu movie), without "modernizing" catholicism, I have very little faith (pun intended) that William Dafoe (total agnostic, or worse) and LaBeouf can do justice to St Pio.
LaBeouf seems sincere in his catholic journey but then again admits in the interview that he loves "immersion acting". Connecting with a character, even with a saintly priest, does not make a conversion. I hope that personally he gets some benefit and it's lasting.
But as for the movie, even if LaBeouf acted perfectly, the director/writers who aren't catholic will have the most control on the (probable) anti-catholic message.