I have a set of solutions that build a complete .NET Any CPU application. I have a WiX project that will deploy that application as x86 and I can run this all manually in Visual Studio 2013 without any issues. Now I'm trying to get this to work in MSBuild / TFS. The conflict is that I need to specify Any CPU for the code and x86 for WiX. My initial thought was to just hack the WiX solution / project to be Any CPU in name but let it actually make an x86 MSI. However the wixproj setup won't allow Any CPU to be used. I would expect the same issues with Any CPU and a 64 bit installer. WiX seems determined to not allow Any CPU.
The remaining option that I'm seeing here is to not build the WiX part with MSBuild but instead handle that in a post build batch file. However it really seems you should be able to deploy Any CPU code with WiX.