This is an interesting study, but the limitation is that the chosen strength-training methods (leg press, leg curl, and knee extension) don't allow loaded stretching. It's likely that there wouldn't have been an additional benefit if the exercises allowed loaded stretching and slow eccentrics in a full range of motion.

Two other critiques: 1) n=16 in each group seems pretty small, though the difference is fairly large and clearly significant. 2) The stretching workout seems like a separate body-weight workout (30min of repeated movements, 10s stretching) 2x days a week, meaning the groups weren't volume-matched. Reading up on it, it's likely that the eccentric loading of the muscles likely results in their findings.

That study uses separate workouts two days a week, for 17 muscles, which is much different from doing some static stretching before a run. They show improved athletic performance for their stretching protocol in a separate article.