I found the study itself quite interesting. The full text of the study is available at
http://jap.physiology.org/cgi/content/full/98/1/93#F2Executive summary of details left out by the article that I think are relevant. They did leg extensions for the training. The Low (glycogen) leg did 1 hour, then no food while resting 2 hours, and another hour. The High leg did 1 hour, then 1 hour the next day while the Low rested. Repeat the cycle. Maximum power increase was the same. However time to failure at 90% of maximum power went up from 5 on either leg untrained to 11 on High and 19 on Low. Also the levels of glycogen after training were higher prior to the start of exercise in Low than in High. What is interesting is that lactate, epinephrine, and norepinephrine levels were higher in the Low post-exercise after training.
The authors of the study say that since the intensity was high enough in the 90% power to failure test, glycogen levels should not have been a factor in reaching the failure. However, here is what is interesting. It seems that the Low leg did a better job of pushing itself (evidence being higher levels of lactate and epinephrine/norepinephrine). It outperformed the High not because of aerobic superiority or increase in strength, but because it just learned to push itself better.
I am willing to believe that the higher glycogen levels lead to being able to push yourself better. I know from experience that the first sign that you are going to hit the wall in 5 miles is that you lose your ability to surge and start struggling on hills.
As far as recovery runs, the study is rather inconclusive. Leg extension does not quite carry over into running. The aerobic component does not play a factor nearly as much as it does in running. In fact, one interesting thing is that the High leg seems to have developed better aerobically - lower lactate at the same intensity. But it was still failing miserably compared to Low in 90% max power to failure test.