Should the MacBook Air have the same amount of charge as its stated capacity when 'Full Charged'? The following is an extract from System Information (under power):

 Charge Information:
  Charge Remaining (mAh):   6517
  Fully Charged:    Yes
  Charging: No
  Full Charge Capacity (mAh):   6690


Is this simply an example of the charger not topping up the battery to conserve cycles, poorly calibrated battery or an issue with my machine's battery?
"Fully charged" does not mean exactly 100%, but somewhere between 95% (or even less) and 100%. Obviously it is better for battery life if the battery is not immediately loaded after a small percentage of charge was consumed, if your MacBook is connected to the charger. So you do not have an issue with your battery.