just to summarize discussion from #modeshape:

• structure of magnolia-nodetypes.xml is JR specific and not JCR compliant. There are few things that need to be fixed such as according to JCR multivalue properties such supertypes should be encoded in single value or can be ignored by repo (which is what MS does). (see JCR 1.0.1 6.4.2.5/Export)
• CND notation is supported by both JR and MS and doesn't suffer from such issue
• Our node type structure also exposed some bugs in MS, so their dev team converted our definition in CND (http://jackrabbit.apache.org/node-type-notation.html) notation supported by both JR and MS and included it in their test cases http://anonsvn.jboss.org/repos/modeshape/trunk/modeshape-jcr/src/test/resources/magnolia.cnd

... since the CND is more readable then xml I would be in favor to abandon the xml and use CND from now on.

Reference to the spec for CND:
http://www.day.com/specs/jcr/2.0/3_Repository_Model.html (section 3.7.9)
http://www.day.com/specs/jcr/2.0/25_Appendix.html