The new scoped jndi does not work with jotm, in particular xapool has problems. This is because the XAPool StandardPooledXADataSource implements ObjectFactory in a non-optimal fashion. The implementation requires that the jndi name of the StandardXADataSource for which it is pooling is set, so it can do a lookup on it. However, it does not construct a new StandardPooledXADataSource object, but rather just sets the results of the lookup on itself, which is odd because it was already constructed with the instance of StandardXADataSource that it just looked up.
In any case, this does not work well with the new scoped jndi naming. This is because objects are now stored in a scope, thus their name is no longer just the simple jndi name supplied by the user.