In the case of nested domain models with intermediates that are not represented in elk (e.g. GCompartments), there is a mismatch between GModel and ELK graph element hierarchy.
When applying coordinates from ELK to the GModel, this is accounted for - the ElkLayoutEngine.transfer*Layout methods call getOffset to transform to the correct coordinate system.
The reverse direction does not - the GModel coordinates are simply copied over to the ELK node. Simply subtracting the offset in my inherited LayoutEngine fixes any visual distortion.