Just for completeness, the "VM"s in this article have nothing to do with containers. But of course we all read the article before commenting and we all know that, right?

Without being an expert in virtualization or containerization, it seems pretty obvious to me that if a certain instruction causes thermal throttling, then that'll cause thermal throttling whether the instruction is issued from a host OS or a guest OS or for any other reason. Indeed, the more layers of abstraction involved, the likelier you are to hit the problem.