In the past we had some hard to diagnose issues like https://bugzilla.xamarin.com/show_bug.cgi?id=38813 where reference assemblies were inadvertently used during runtime.
We should add proper validation so that we abort early and with a nice error message when Mono tries to use reference assemblies instead of the implementation assemblies (whatever the cause is, because this is never valid during runtime).
Right now, we only run cil-strip on the implementation assemblies to generate the ref asms which just empties method bodies, so it could be a bit more difficult to tell the assemblies apart. But we should at least assert that some fundamental types in corlib have method bodies.
In the future, it might be a good idea to annotate our ref asms with the [ReferenceAssembly] attribute (see https://msdn.microsoft.com/en-us/library/system.runtime.compilerservices.referenceassemblyattribute(v=vs.110).aspx) so we could more easily detect and deny all reference assemblies.
Issues like https://bugzilla.xamarin.com/show_bug.cgi?id=42584 (and numerous others) would be way easier to diagnose if we had this.
CoreCLR does the check here: https://github.com/dotnet/coreclr/blob/775003a4c72f0acc37eab84628fcef541533ba4e/src/vm/pefile.inl#L139-L148
*** This bug has been marked as a duplicate of bug 42584 ***