Per AppDeploy, under CustomAction, if you change the target in setPROFILE from:
[%APPDATA]\Macromedia\Shockwave Player\
to:
[AppDataFolder]\Macromedia\Shockwave Player\
it'll do what Adobe/Macromedia intended during a GPO install.
I have noted that the fix works great for IE, but doesn't install the plugin for Firefox. Others have noted that they were unable to get the MSI to work, but I'm kicking it now, so we'll see.