Fixed #5299: boxes created for links in PDFs were misplaced.

This was because of the use of the incorrect transform matrix (SVG's instead of Cairo's).

I also reverted some refactoring from the commit 1a93996b which introduced the bug. I believe that this refactoring is rendered useless, but most importantly is confusing (a line of comment was removed in the refactoring and also the getItemTransform function is not documented and can be confused with getTransform).