Assembly.ReflectionOnlyLoad does not inspect the publishers policies, but requires that the exact version be present on the system. Assembly.Load DOES inspect the publishers policies and will allow a binding redirect.
 
The DirectoryModuleCatalog does a ReflectionOnlyLoad in order to determine which modules are available in the module directory. The use of ReflectionOnlyLoad puts a restriction on module loading that any referenced assemblies must be the same version that it was built against. Even though during a normal Assembly.Load it may successfully bind to a more current version. This is true with .NET core assemblies like System.Core.
 
DirectoryModuleCatalog could change to use Assembly.Load instead of ReflectionOnlyLoad. The ModuleCatalog uses a temporary AppDomain and disposes it after discovering all modules, so there shouldn't be a concern of assemblies being left loaded. I have done this in a local copy of Microsoft.Practices.Prism.dll and this seems to correct the problem.