Our PowerMap JDO product has specific features for database integration and transparency to existing RDBMS/ applications. These are standard capabilities and can be used within Java, Tomcat and servlet, or J2EE containers.
Enterprise Edition also includes a JCA resource adapter. This is an optional developer tool, enabling automatic transactioning & enlistment within the J2EE transaction.
Most projects just use the 'explicit' approach and request transactions from code, this seems to be the more popular technique as as most shops do not require the RA.
As you said, JDO is using the system contracts of JCA to integrate within J2EE App Servers. I'm not aware of any JDO implementation able to use the CCI part of JCA to access Legacy Data Sources.
This will be available in LiDO from xcalia in Q2 2005. Even in that case you will still need a JCA connector on top of which LiDO will do the transparent mapping, exactly as ORM mapping tools are built on top of JDBC (and you still need a JDBC driver).