Because it can't be done that way. Hdds are encrypted to that console only and cloning doesn't work unless done with the console.
I can't remember what I transfered when I done it (it was years ago) but I don't remember there being a limit for selection as I got everything and I did have to leave it overnight to complete.
As regards to moving and not copying... I ensured it all copied across first before deleting from the old hdd... Just to make sure i didn't lose anything!