For the iPhone 6 and 6 Plus they are replacing the whole phone still. However, for older models it may be possible to have them just swap out the screen. I don't think you will know until you get there, however if you don't want the whole phone replaced you would have the option of backing out last minute.
To me having a replacement phone is a nice perk especially if the phone is a little bit older since you get a new battery and other new guts (basically resets the clock on the inevitable failures), especially since if its just broken glass they will charge you a broken screen fee instead of a whole out of warranty repair fee.