Really, this looks fine. I've seen a pile of metal roof in rural ag areas, and this is the right boot, done the right way. Yah, if they'd thought ahead they might have been able to schedule the sheets to not land on the seem. But putting the boot at 45* and screwing them on either side of the seam is correct, though that bottom one is squonky, but it's at the bottom so it shouldn't be an issue. Proper caulking under and around. This is probably as good as it gets.
