I'm unable to say exactly where the problem is, but I basically created mockup interfaces with identical declarations, generated xmldoc and copied the generated method definitions into the annotation xml. I also redid the complete annotation file starting with a blank xml file.
<assembly name="NHibernate">
<member name="M:NHibernate.IQueryOver`1.List">
<attribute ctor="M:JetBrains.Annotations.NotNullAttribute.#ctor" />
</member>
<member name="M:NHibernate.IQueryOver`1.List``1">
<attribute ctor="M:JetBrains.Annotations.NotNullAttribute.#ctor" />
</member>
</assembly>
My above try-everything-approach should have matched, but didn't. I guess there were some issues with whitespaces or just bad luck.