Interesting point. However, the study you're citing doesn't really contradict the strong correlation between MCAT and STEP scores because your study is looking at the success rate of MS1s moving to MS2 year, but Step 1 isn't taken until the end of the second year. Also, passing your first year is different than scoring high on the standardized exams, which (unfortunately) is something schools care a lot about.
It definitely sucks, but to echo what
@TravelingMedicine said, simply coming to terms with the fact that the process may be unfair and in part a matter of luck has personally helped ease my frustration and anxiety.