They probably just remastered the original masters.
I noticed that on the original 80's CD, if you skip to "Stay", you can just hear the end fade of "Pretender" before the song kicks in. The remaster omits that. Random fact for you...
I read reviews on Amazon for "Madonna Remastered" and they were all whining that Holiday was the 7" Edit and Borderline was an extended mix and it was the alternate mix of Burning Up and all this other stuff which, naturally, made me double-check my copy, and nope, everything the same as the vinyl edition. How odd.
Dunno about the back-cover of Like a Virgin. The copies I have are both the lacey ones. Hmm. Have to double check.