No, JDO allows you to specify the mapping between the DB schema and your object model. It is more work, and I certainly enjoy the freedom of being able to introduce new persistence capable classes and needing to write only a trivial mapping descriptor (e.g. <class name="Letter" persistence-capable-superclass="ItemImpl"/>)
I think there will be cases when it is appropriate to do a fully specified mapping of your objects to your schema -- for instance, if you ever decide to change JDO vendors you would either need to export and import your data, or set up the same mapping for both JDO implementations.
What properties of the default mapping which your JDO implementation uses do you see as making the schema inappropriate for use from other languages?
I don't think that lack of control over schema mapping in JDO is a valid reason for using entity beans, although this will depend on your vendor. I've only used Solarmetric's Kodo, which does allow you to control this mapping.