I do that all the time, but with step/wrl combination. The result can be seen in Designing a multiple levels PCBs in KiCad? - #5 by eelik.
Workflow, simplified:
- Import an existing motherboard into FreeCAD StepUp.
- Export it to KiCad-compatible step and wrl.
- Add those to a footprint which has the motherboard features as graphics (maybe pads, too).
- Add the footprint to a “shield” design.
Now you can see both boards in the KiCad’s 3D view, nicely rendered. I think the most difficult part is mapping step colors to wrl colors in StepUp. And for this to work the step models must have colors.
After that you can of course export the whole as VRML from KiCad, or import the board to FreeCAD to export it as step/wrl again.