We've just removed the configuration in the server.xml for specifying the context entry (CE) for a partition. There were issues with implementing this with XBean - it was very messy too. Instead we now defer creation of the context entry until after the server is started. So the partition is created and present yet it does not have the context entry which makes it not seen even though the entry is listed in the RootDSE under the namingContexts attribute.
It's disappointing to fire up the server and notice your namingContext is missing for a new partition you added. The first thing the user feels is that there's something wrong with the way they configured their partition.
Rather than omit the CE, I suggest we have the partition infer a context entry based on the namingContext DN's RDN attribute. Partitions should be able to accept a CE in which case the inference process is bypassed. If omitted though the CE is inferred. Some examples: