This may be unique to my situation in that I import the Gerbers into CopperCam (for milling my PCB’s).
Hopefully I can get pointed in a direction to resolve this but, I can live with the current outcome…
My attempts to resolve included various settings and Origin usages in both KiCad and CopperCam.
The current, Dialed-In (KiCad) settings and results, are very good and my only complaint is an Offset of the PCB’s perimeter (Edge-Cut) that happens when loading a layer containing the Perimeter Shape.
The cutouts and graphic holes are on User Layers. Results are Perfect!
The PCB shape is on the Edge-Cut layer. Results are an Offset Shape Contour.
If I draw the shape on the User Layers, those layers get Offset (just like the Edge-Cuts).
[Note: was able to make/include rectangular cutouts for Flat-Contacts on Barrel Conc FootPrint (Very Cool - Thanks KiCad folks!]
I use the Offset feature in CopperCam to correct the Edge-Cut layer. It’s a minimal extra step.
[click to expand the image] if needed