The original scope of the AOP plugin was to support "one AOP descriptor per project". The AOP developer meta-model is pretty heavily dependant on this model ATM, and it will take some changes to make it support multiple descriptors, but the feature is on the table for an (as of yet undetermined) release.
On a side note, your problem is actually just related to some extra code we have for manipulating the jboss.aop.path at AOP application runtime. Would you mind opening a JIRA task for this problem?
Is it a problem to merge the contents of pat-aop.xml and jboss-aop.xml in the meantime?
Merging the contents of pat-aop.xml and jboss-aop.xml is no problem. I posted the JIRA task.