I have received the confirmation from our developers:
Overlapping skin-end and skin-separator lines behave differently in floorplan wall junctions and sections. In the former situation, skin separators win, while in the latter, there are other complex rules. But what's important in this case is that thicker lines win.
As far as I know, this is a complex design issue even if we only consider the use cases and compatibility in one of the view types. The only workaround, which has been mentioned already, is to use the same thickness/same color lines for the different settings, but we understand that this is not the desired option.
For further development, please refer to it as DEF-6689.
I hope that it will explain the situation here. I'm very sorry for the inconvenience, and thank you very much for your understanding! Feel free to ask if you have any further questions!
Technical Support Engineer