Free transform poses problems when pasting into multiple documents though. For example, when creating graphic email footers, they all need to be exactly the same size. If I paste from ID into a correctly sized PS doc and they appear smaller, I then have to manually enlarge them all by eye which will result in them all being slightly different sizes.
The fundamental problem is the difference in the way CS3 and CC act when copying and pasting. I don't know of it's a problem with copying from ID or pasting in PS, but the CC method just isn't as usable as the old version.