It's because you get free energy when your energy is below your cap.  

If your cap is 100, as an example, and you have 70 energy, then you will gain free energy per so many minutes until you reach that cap.  But if you have 100 or more, you will not accumulate free energy until you go below that cap.

If your cap is 100, use it up before you accumulate 100 to keep accumulating free energy. 

This is very important for F2P and for optimizing your resources.  

Simply, because if you have more than the max capacity, you won't earn any more energy from time passing. You get one energy every three minutes, or 20 per hour, just for doing nothing. Over the course of the day, that translates into up to three full refills that you are missing out on, if you go over the energy cap.