I just purchased a Macbook Pro Retina off of the Refurbished Store for $1,269. It only has the 128GB SSD. I called up Apple and let them know that since it was Refurbished I was not given any upgrade options, and what can be done about upgrading the SSD since I feel that I really need 256GB. Apple let me know that I can purchase the SSD from them for the $200 and then have it installed by an Authorized Apple Service Rep. Apple themselves will not install the SSD, but in order to keep that warranty in effect I have the option to take it to an Authorized Apple Service Rep.
Apple Support referred me over to Mac Works in the Austin, TX area. I contacted Macworks and let them know that I already have a 256GB SSD and I want to know the pricing to have it installed. Macworks will install the SSD for $120. There you have it.
If you want to upgrade your SSD and keep your warranty then just pay $120 installation fee and have an Authorized Apple Service Rep install it for you. Apple will accept this installation without voiding your warranty.
Upgrading the SSD is very easy, so it's up to you to decide if $120 is worth a few screws and keeping your warranty. To me it's worth it since I have a Refurbished Mac and definitly don't want to void the warranty at all. I have no idea how these Refurbs hold up over time.
Apple Support did not advise me if the installation had to be an Apple SSD or if 3rd party SSD such as OWC will be okay, but the Support Rep did say that there shouldn't be any issues.
His exact words were, "If you want to upgrade the SSD then there is no reason why installing that upgrade will void your warranty. Things that will void your warranty would be spilling beer on your Macbook."
Bottom line: Yes you can upgrade your SSD, but it'll cost you the cost of the upgraded SSD plus $120 to have an Authorized Apple Support Rep install it for you so that your warranty will not be void.