It shouldn't make a difference, if CSS transforms is applied via the style attribute or the style element to an element in the DOM. And there is also no visible difference, but the style.webkitTransform is different. On applying the transformation to the style attribute of the element, the CSSMatrix has correct results, applying the transformation via the style element gives back the identity matrix. I'll upload two examples. Bot shouldn't give back the identity matrix.
Created attachment 58348 [details] Test: gives back correct matrix
Created attachment 58349 [details] Test: gives back identity Same example as the previous one, but setting CSS transforms for all div's in the style-element. Notice, that the visible results of both tests are the same.
element.style.webkitTransform just returns the inline style. You need to use getComputedStyle() to get the actual style.