I know this is old but since I found a solution after looking here I thought I should provide an answer. VS 11 holds the publishing app_offline.htm
file in this location:
C:\Users\[user]\AppData\Roaming\Microsoft\VisualStudio\11.0\app_offline.htm
I have tested this and customized it and it does work if you change this file. The down side, of course, is that this is the file used for all web publishing.