Actually, the solution is fairly simple, if not cumbersome ... and may not necessarily work for you.
What I do now is to obfuscate each of the assemblies that I reference in the main Outlook add-in, and reset the references for those assemblies to the obfuscated products. I do NOT obfuscate the main add-in assembly. This way, the manifest generated during the Visual Studio build of the main add-in assembly is calculated against the actual assemblies used. For us it works beautifully.
This works if your main add-in assembly does not need to be obfuscated, but only the lower-level referenced assemblies. If you have things in the main assembly that you want obfuscated, you could refactor those things into another assembly.