"Why would running cause a physiological adaptation that was bad for running?" Hmm, so I guess all of the physcial therapists and everyone doing core or hip mobility, weights, even plyos are hurting themselves. I realize I'm getting off the topic of stretching, but I'm trying to show evidence that this is false. As I understand it, strong muscles in one area can mean a muscle imbalance which leads to a change in how muscles and joints function, so strengthening "non-running" muscles can be helpful.
I always wonder about how these studies are performed. Perhaps those with less flexibility were already the strong ones. Makes sense to me. Perhaps they were more economical not by being less flexible but by being stronger/having more experience. Or perhaps there's some other underlying factor. (Correlation doesn't mean causation!)
I agree with the idea of not stretching cold, but sometimes on a run I wonder why I'm feeling so stiff at the beginning and I realize I had to cut the stretching after my last run for the sake of time. I don't always feel it, but sometimes I do without going into the run thinking about the fact that I didn't stretch afterward last time. But I also don't stretch hard, but for a longer time than most (1 min per stretch, easing into it). Maybe I'm not as fast today as I could be without stretching, but I think I'm faster over the years from it.