There are JVMs that run in bare metal, specially in the embedded space.
This was also the Lisp Machines and Smalltalk.
Native Oberon and AOS are also two systems were the language and OS follow the same principles, although the code is usually compiled to native code, or JITted on load.
For the same reason Lisp Machines had issues with their special processors.
It is a fallacy that those instructions help execution, in the end general purpose processors are quite capable and you just need a native code compiler instead of trying to execute the bytecodes directly.
So most JITs on ARM just take advantage of the native instructions, or you just make use of a native code compiler for Java if required to do so. Although the general public seems unaware of it, many Java SDKs for the embedded market also offer native compilers, even Oracle does it.
This was also the Lisp Machines and Smalltalk.
Native Oberon and AOS are also two systems were the language and OS follow the same principles, although the code is usually compiled to native code, or JITted on load.