Reviewing what I was doing and some more experimenting, I realized what was going on (did not fully understand it in my replies above). The rotation angle mentioned applies to the 3D model and not the footprint orientation and is of course available in the tab for the 3D model. What was did not appear to me was that the rotation angle of the 3D model affects the way the footprint is oriented when imported into StepUp, as after I corrected the angle I only thought it would affect the angle in KiCad, thus I did not save after resetting the angle before importing into StepUp.
Although I understand why it doing this, quite frankly I am not sure StepUp is working optimally by changing orientation of the footprint at import based on this angle. It would be safer to always stay with the orientation of the footprint seen in KiCad so that the 3D model can be aligned to the actual footprint orientation, forcing one to always use angle 0, scale 1 and offset 1 for all axis in the KiCad 3D model setup. At least this is how I assumed it was working from when I started to use StepUp until this post. It is not a problem though now that I understand how it is working, I must just make sure that these values are reset before the footprint is imported into FreeCad with StepUp.
I had some fun getting my custom library updated with Step models in addition to the wrl models during my recent reorganisation. While the project below is is the very first project I did in KiCad as a learning experience - it is a signal generator I built on a development board/breadboard to learn how to use DSP functions of the dsPIC30 microcontroller and the components were basically just transferred from the breadboard to the PCB, so not a showpiece from a design perspective, I think the through hole components look very good in 3D and made it worth updating this project just for showing off. (And this is where I used the angled 3x2 pinsocket. Later projects use mostly SMD though).
The boards with the buttons and the rotary encoder were separate projects exported as STEP to FreeCad, and the aligned to a footprint as step and wrl models using StepUp. The SparkFun enclosure was also associated with a footprint. Here is the view in KiCad using the WRL models; the MCU is on the other side of the board under the display
Same project imported into FreeCad with Stepup based on the step models, here in orthographic projection (and edited to get transparency of the enclosure back).[ KiCad native export gives very similar result.]
A couple of views without the enclosure in FreeCad:
So, yes, I am making very good use of StepUp!