Answer: The framework uses the specific installer for the build you are targetting. ie. if you have built an x64 framework and run on a 64-bit OS, it will use the Framework64/InstallUtil. If you have targetted a 32-bit or Any CPU build and run on a either 32-bit or 64-bit OS it will use the Framework/InstallUtil.
Note: a 32-bit build installed on a 64-bit OS will still use the Framework/InstallUtil. there is no workaround - you cant have a 32-bit installer install a 64-bit service. You have to build a separate x64 installer if you need to install a 64-bit service.
Source - Microsoft Forums.