A bastion of scientific thought, Runner's World isn't. There is no research or schooling that I have seen or heard of that rest position could effect the benefits of exercise, with the exception of maybe recovery time (if one was to "rest" in a particularly blood-restricting manner).
That mayo clinic study seems to say that after adjusting for exercise duration, people who sit more are less fit than their standing/walking brethren. I have seen sloppier comparisons made, but only a few. The full text is behind a pay-wall, but I think this is just another "duh" moment in research.
Scientist: Are you fit?
Average Rube: Yeah!
Scientist: Do you sit a lot?
Average Rube: Yeah!
Scientist: You would be more fit if you sat less!
Besides the fact that the difference between a true high mileage or competitive runner and just a normal "fit person" is like comparing.... two... really incomparable things(?)... how they presumed to quantify not only how much "gainz" you lose, but how much you gained in the first place is absurd. Individual difference in response to exercise are VAST and anyone who tells you that you would get "Two running points faster" for a particular workout needs to be gently patted on the head and applauded for their video game-esqe idea of how "leveling up" works. It's cute, but grownups are talking now, and they should go play with their blocks.
But take all that with a grain of salt, because I'm just some dude on the internet.