As the Microsoft FxCop libraries are inherently 32-bit (including native code as they do), developing code using them on a 64-bit platform throws up places where the modes get mixed, and an assembly that is generally AnyCPU ends up needing to load an x86 library and barfs. No real problem here, use
corflags assembly /32BIT+ /Force, where you need the /Force for a strong-named assembly. And then if later you need that one strong-named... There is the standard technique of ILDasm/ILAsm to rebuild the assembly with strong-naming (as documented e.g. here), but you still end up with the corflags yellow warning in the MSBuild output about breaking the original strong-naming if you need that too.
But when the code I was working on also uses Mono.Cecil to do stuff, it was easier to silently do the whole lot in one script:
Yes, you can do that in PowerShell too, just with more fussing about the path to the Cecil assemblies because of the schizophrenic current directory model it has. And because the rest of the code in this particular project is F#, keeping the build scripts in the same language is just natural.