I suspect the problem lies with the following part of your StandaloneSetup bean config:
Do one of these .ecore file have "http://www.myproject.de/mycompany/MyModelEd/model/V1.1" for nsUri?
The registerEcoreFile property causes the specified .ecore file to be loaded as an Ecore model, instantiated as a dynamic EMF model (through the dynamic implementation of EPackage hooked up to a generic/dynamic implementation of EFactory) and registered with the global EMF registry.
However, later on you refer to your "ModelPackage" using:
<metaModel id="mm" class="org.eclipse.xtend.typesystem.emf.EmfMetaModel">
This will ignore the previously registered dynamic version altogether and just look at the static EPackage which has its own static EFactory implementation.
Now the type system doesn't recognize that we're dealing with the same meta model, which eventually causes the Exception. The solution is to use one way of referring to this meta model: either through the .ecore file or through the static EPackage implementation.