Not really talking about the Gerber files. Every board needs to be mounted and often they have connectors which have to line up with the openings in cases. I've even seen connectors that are fastened to the case as well as the PCB. In those cases there has to be a common framework for communications.
That's what I'm asking about. Do people have problems when the PCB layout tool uses a different frame of reference, or is that already worked out?
I regularly import the STEP files of board assemblies generated by Kicad into Fusion360. I'm still on 5.1.9 which uses the "Y increasing as it goes down" TV raster format.
There's always some fussing with orientation. F360 has the "top" of an assembly parallel to the X-Z plane, with Y increasing up. See the picture. The imported STEP files seem to have the positive Z axis going up, with the plane of your table (say) as X-Y.
Of course the PCB assembly is "correct" and not mirror image or inverted somehow. It just has to be oriented as you need. So it's always fun to import, say, a STEP model of a Hammond extruded enclosure, and then import the PCBA model, and flip and rotate one with respect to the other to get them lined up.
Now further on this, I have a 3D printer, which is handy for making enclosures. The printer considers the plate to be the X-Y axis, with the origin to be (as you face the printer) the left front of the plate. The Z axis is up. And every time I bring an STL from F360 into Cura for slicing, it has to be flipped/rotated and aligned on the plate. [attach=1] What Fusion considers the "top" and how Cura views the print surface are different.
So all of this is to say that origin and direction just seem to work themselves out.