Hi,
Thanks for getting in touch. This is a tricky issue to solve, it's caused by the fact that the two segments are different depths. In order to ensure that the corners are beveled correctly, different slices distances are used by the corner algorithm. You can override this by using a compose operator with the corner segment in the 1st and 3rd input and a null segment in the second. The null segment, falling perfectly in the middle, will be used to center the composed geometry on the corner. This will ensure that the corners align, but it will also mean that gaps might appear at the corners because we have overriden the automatic algorithm. To fix it, add a Fixed X Size to the Null segment, and then increase the generator's Rules > X Corner > BC Offset value until the gap is closed.
Please see the attached file for a possible solution.
Many thanks,
Paul