> Thus, it affects the rendering of an element, but not the element's inherent geometry
Maybe you want to use the geometric bbox mode in Inkscape (the one which shows the geometric boundaries, not the visual ones): the geometric bbox of a clipped object is as described in your quote. The visual bbox on the other hand includes the visual i.e. clipped part only.
> Thus, it affects the rendering of an element, but not the element's inherent geometry
Maybe you want to use the geometric bbox mode in Inkscape (the one which shows the geometric boundaries, not the visual ones): the geometric bbox of a clipped object is as described in your quote. The visual bbox on the other hand includes the visual i.e. clipped part only.
But maybe it's me misunderstanding the spec.