There is an important SIF orientation consideration when you do manually what FEA Tools does automatically. When modeling from the center of the intersection to the surface of the run pipe where the branch connects to the header (with either a weightless rigid or a pipe element), you will have only TWO elements connecting, not three. In this case, the in-plane and out-of-plane direction may not be the same as the actual fitting, because at the two-element junction, we no longer "know" what the fitting orientation actually is. There is a convention that CAESAR II applies in this case, and if you don't know what it is, you can accidentally input the wrong values! If you don't know the convention, the conservative approach is to put the highest SIF value of the two in both in- and out-of-plane directions.
Here's the convention:
If the two-element connection is vertical, then the in-plane bending axis is the X-axis, and the out-of-plane bending axis = Axial x In-Plane.
If the two-element connection is not vertical, then the in-plane bending axis = Axial x Y, and the out-of-plane bending axis = Axial x In-Plane.
Just one more reason why it's better to have FEA Tools do this conversion for you.