In my experience, the equal but opposite angles theory is a basic starting point - Eg: trans at 3* down, Pinion at 3* up, or vice-versa. But in practice, sometimes that doesn't work, and the final solution may be something so out of whack from that theroem that it will cause an engineer palpitations. I have set up a lot shaft operated equipment, with just about every, and any type of flexible joint, and seldom has the equal and opposite idea been the true final solution, only the starting point. So, in reality, the answer is "whatever works, and works well" - within reason, of course; at some point, the angles will become un-workable.