Interesting effect, wrong explanation
While the code clearly shows a variance in the time, his explanation - that it is caused by variance in the transistors - is BOLLOCKS.
From the article, "CPUs, Roig's paper explains, contain millions or billions of transistors, which have enough variation that no two chips perform identically" This is nonsense. While over-clockers might exploit this to crank a few extra Hz out of their rigs, CPUs are synchronous beasts, so if you run the exact same code on two identical processors, clocked at the same speed, you will get the same result.
The variance will have many sources, from the OS servicing other threads, network interrupts, refreshes on the SDRAM, to caching, but transistor variance is not one of them. If you run this code on a bare-bones processor using on-chip RAM, then I would be extremely concerned if this showed any variance at all.
Ironically, a HWRNG possibly does use transistor variances to guarantee no two generators follow the same sequence...