I ran across this when verifying JBIDE-8863.
When you create an EAR project with EAP 4.3 as the target runtime and not check "Generate application.xml deployment descriptor", it will still create the descriptor.
I'm not sure but perhaps deployment descriptor are not needed from EE 5. So if that's true it makes sense that it gets created for EAP 4.3, but it's still a bug - the checkbox should be disabled then.