They are not differenciating between bits. They are noticing a set pattern of variance of frequency of emmissions by a set of CPU instructions. I think of it like if I was in a car getting driven blindfolded, I could tell if we accelerated, sped up, went up a hill labouring the engine etc. Now if you can measure each of those changes, AND know each road so well you could map your journey. Of course if you decided to do this as a very focused study.. AND no part of the test was being purposely obfuscated..you could probably get surprising results.
further to this, in 2014 there was also work done by the first participant
https://www.tau.ac.il/~tromer/handsoff/ where they do actually get to a bit level