I'm not sure I get the reference? Could you explain a bit? I know what Java EE servers are, but don't recall anything about bare metal deployments. Comparing my experiences with using JEE and Docker was that they are nothing alike. Just unclear as to your point.
Java was at one point going to have a bunch of CPUs[1] built around the JVM bytecode, that would have allowed J2EE and such to run on the bare metal hardware, but they largely didn't go anywhere.
The most successful attempts that i'm aware of are Jazelle[2] and Java-card[3] plans to augment the software solutions