How are all these VMs going to react if people switch, say, to desktops with ARMv8, or whatever comes next?
There are perfectly functional x86 emulators for ARM already. Many people used to run Windows on PPC macs via emulation too.
It's not my area of expertise but I expect to see something similar here. If you need to emulate hardware you might take a 10x hit, which might be unacceptable for very large scale computations. But in the longer run that might not be a problem as more resources become available.
As I say, I (and many other people) emulated x86 windows on PPCs for years. I ran visual studio and it dragged a little, but was fairly usable. Certainly it won't be as fast, but then again by the time x86 has died and people have moved, hopefully systems will have got fast enough to make up the difference!
There's a risk that the VM platform decision could date and, ultimately, render useless an experiment sandbox.
However, two points. Firstly, any attempt to wholly encapsulate an experiment will be susceptible to problems concerning the technology choices made. By choosing the abstraction at a VM level, you're more likely to get a better number of years out of your choice than picking specific programming languages (which I contend would fail to gain adoption as researchers wouldn't change their obscure toolkit if they felt it was the right one for their research).
Secondly, even a VM for an obsolete architecture is better than what we have today - the original paper and perhaps an email address for the lead author.