It seems the (very cool) Web Inspector does not look at the transform when drawing an element highlight. I have an experimental solution via an absoluteBoundingBoxRectWithTransforms method, and have that called by WebCore/bindings/objc/DOM.mm and InspectorController::drawNodeHighlight However, this doesn't work for text runs within transformed elements. I'm sure you'll come up with a better solution anyway :)
<rdar://problem/5853507>
Fixed by the patch in bug 21942.
Fixed by the commit for bug 21942.