Hello Morgan,
we do not incorporate the obfuscation process in installation packages. Here's a rough list of the steps we do :
1- Build the assemblies
2- Obfuscate them
3- Add the assemblies in the Setup Project (manually, yes)
4- Build the Setup project
We use InstallShield for our setup projects and we have a batch file that launch the obfuscation process and resign the assemblies (Because they cannot be signed to obfuscate them).
Alex