Hi Danny,
I can't speak for bertol, but there are a couple of scenarios where you could want or need to make this adjustement:
1. To take into account the real eccentricity of the joint in the calculation.
2. To show the relative position of both frames but without considering the eccentricity of the joint. In this case you have to select the option "Do not transform frame stiffnessfor offsets from centroid": You´ll just get a aesthetic implementation without any further impact in the calculation.
I hope this clarifies your doubt. If you need more details you can consult the SAP manual.