Hmmm, they didn't verify the correctness of the translator or CLR?
The way to verify the entire system is not to verify that quantum physics works; that doesn't help. Instead you have to assume that the logic gates you are using are deterministic which is impossible to prove. Then you work up from there.
Despite this, I do agree that having part of the system verified is better than having none of it verified.
There are other folks who have successfully done formal verification of operating systems, device drivers, hardware design, etc. It's a big, hard problem, but we'll get to the "whole stack" eventually.