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Since JEE6 there is more standardization for JNDI resource naming. But before that it was a giant mess, yes. The first way to combat such issues that was introduced with JEE5 was the addition of resource injections to not have to do manual JNDI lookups, in stead the container deals with that stuff for you. But injection was only possible in container managed resources, so it wasn't automated away entirely.
In any case, the "problem" is not so huge that you have to start thinking people are kidding you. Believe me, there are far worse issues you'll run into when migrating from one container to another when you do more than basic web stuff with a single persistence unit.
Yes, I totally understand that there are several problems when moving from one container to another one, but it felt a bit ironic that the standard for naming resources does not have a standard for naming the jndi resource it self.
But I agree that it is not a huge problem...