The latest transforms spec says that the background of the root element that has been propagated to the canvas isn't affected by the transform on the root element.
The compositing spec describes the 'Root Element Group', and says that filters on the root element should be applied to that group, which includes the (untransformed) root element background.
I believe that means that we're applying the filter to the combined untransformed background + transformed page content.
However, the filters spec for the filter property explicitly says that the filter operations are applied in the element’s local coordinate system.
It seems like these are directly in conflict with each other, and we need extra clarification on what should happen for the root element.