JPA does not limit number of persistence units defined in persistence.xml. This warning just tells about limitation of tool in Eclipse IDE. This is told for example here http://www.eclipse.org/webtools/dali/gettingstarted.php :
Currently Dali only supports one Persistence Unit and one Persistence
XML file per project. Other configurations can exist in a JPA project,
but the validation and defaults processing may not be correct when
multiple persistence units are used.
I guess there is no known way to get this work in Eclipse IDE.