The study makes a lot of sense. The body is all about survival, which means increasing efficiency any way it can, whether good or bad. Do what it takes to survive and that's it, nothing more or less.
It adapts in a way that allows it to be more effecient, decreasing energy expenditure any way possible. So in this case, tightening up the muscles and tendons allows the tendons to absorb and release greater elastic energy than before, reducing the need for active muscle contraction. In other words it allows the runner to bounce along using a more "rubber band" effect and saving the runner from having to supply energy to actively contract the muscles harder on each stride.
The body doesn't care if this is bad for the joints, it only cares if it is conserving energy for the more vital things (heart, brain, organs, etc.)...for, again, survival. It's why when doing training of any sort we have to follow the principle of progressive overload. Our body adapts to training with the bare minimum, so in order to see gains we have to progressively attempt to do something more or faster or higher.
Tightening the joints and muscles isn't necessarily a good thing, depends on the situation. But in this case the muscles gets smart at the expense of the joints. If I was a runner, which I am not, I would still want to work on my flexibility to maintain my joint integrity and overall health.
Our muscles, joints, and systems are extremely smart, it's our decisions of activity that mess things up.
The body is always smart, it's just that sometimes are brains can be dumb.
Aaron S