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For transform, transform-origin, and perspective-origin, Percentages says "refer to the size of the element's box". This isn't clear: which box? It should say "refer to the size of the element's border box", as in the merged Transforms spec. (This is still not perfectly unambiguous, because it's left implicit that X values are relative to the width and Y values are relative to the height. This is in contrast to the padding property, for instance, where all percentage values are relative to the width of the containing block. But it's probably good enough.)
(Note that at least Gecko doesn't actually use the border box of the element for perspective-origin -- it seems to use the border box of the first *child*, or something weird like that. But WebKit seems to use the border box of the element, as expected. See <https://bugzilla.mozilla.org/show_bug.cgi?id=721082>.)
Combined spec now talks about the border box.