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Their "concrete instantiation[s] of a micro virtual machine", their reference implementations, are in Java and Scala, which of course run on managed VMs, which makes me at first glance wonder what they think they've demonstrated with these implementations.
I wouldn't place too much importance on their choice of implementation language. I'd imagine the goal of showcasing their reference implementation is to demonstrate the operational semantics of their virtual machine. Equivalent implementations could be produced in C for example.
For those looking for the spec and early impl, see http://microvm.org. The paper says it can currently run simple RPython scripts.