When apple replaces the battery in a 15" MBP retina, do they replace the entire top portion of the case?
It appears to be the case that Apple will replace the top case assembly if you want to replace your battery.


  As first reported by Treehugger, which received a copy of an Apple internal service document for the "Mid-2012" 15-Inch Retina Display MacBook Pro, Apple informs its own service personnel that "batteries must be replaced with the top case assembly" and that "the battery alone is not a replaceable part." EveryMac.com also has been provided with copies of the internal service documents for subsequent 15-Inch Retina Display MacBook Pro models and although there are internal differences, the battery design effectively is the same.
  
  Additionally, Apple warns its own technicians that "batteries should
  not be separated from the top case assembly for any reason," as
  attempting to do so could puncture the battery and lead to fire or
  injury. Do not attempt to pry the battery apart from the top case.


Source:  EveryMac.com

According to iFixit, it will cost local repair shops around $500 to source the top case assembly to replace the battery.  

IFixit.com also has instructions on how to remove this battery should you want to replace it.  Batteries with a minimum of 12 month warranties can be had for $90USD makes this a worthwhile consideration.  Keep in mind that this is a difficult repair and if you are unsure of your ability to tackle something like this, best hand it over to a pro.