Earlier quoted context omitted.
I'm not clear what your point was about the VMs. Why do hypervisors need Meltdown mitigated? I think you're underestimating the % of HPC networks with properly-configured firewalls and only running code from trusted sources.
If you trust all the code (and other inputs, or outputs) on all the VMs, and you are running it in a secure environment, you don't. I admit, it's possible I'm underestimating how common this is. Why you generally do need it is the above isn't true, and microcode has to be loaded at the hypervisor level for everyone or for no one
This is quite common in the engineering/research sectors, which love clusters. Think Sandia, oak ridge, etc. I also personally know of several private companies with research clusters. I'm curious how common hpcs are outside of the research community, because honestly I'm struggling to think of a practical need for one.