The book THE ONE MINUTE WORKOUT. does a good job of explaining what happens at the cellular level when we exercise. It doesn't necessarily have to do with the length of the aerobic workout, it is much more complicated process. But it has to do with your energy demands and your body.
The body has all kinds of fuel sources: ATP, phosphocreatine. Anaerobiv glycolisis, and oxidative metabolism. All are very complex processes, for example ATP is turned into ADP and AMP then AMPK then PGC1. And this all effects whats happening at the cellular level.
In short the demands of running uses a different process that increases aerobic capacity and lowers heart rate, the demands of strength training uses a different process that increases muscular strength & size.
If you're interested, the book will explain it pretty clearly.