The problem here is (apparently) that calls that used to cause Windows to read the RTC now give you a TSC-based time instead. If the TSC speed has changed since boot (which should only happen if the user has explicitly changed the CPU base clock, never under normal use) then you have no way to calibrate the OSes idea of time against an actual time source. This is a problem if you're trying to perform accurate benchmarks when under/overclocking.
So yeah, Windows 8 appears to use the CPU TSC without recalibrating when there's a change in TSC tick rate, but that's because the TSC tick rate isn't supposed to change.
Right - I'd say that the problem they're having is just a bug in the program they use to change the tick rate at runtime, that is, not making the kernel aware of the change. The article is written as if there is something fundamentally wrong with clock implementation on Win8.
Example from article: By underclocking the BLCK of a Haswell system from 130MHz to 122MHz (-6%), Windows 8 loses 18 seconds over a five minute period; and the inverse applies to overclocking, too. This does not apply for Windows 7, which adjusts itself fine.