Reserved instances are applied to running instances in real time, not averaged over any longer period of time. They are baseline, not average.
For example, if you own three Reserved Instances with the same instance attributes and region (or Availability Zone if applicable), the billing system checks each hour to see how many total instances you have running that match those parameters. If it is three or less, you will be charged the Reserved Instance rate for each matching instance running that hour. If more than three are running, you will be charged the On-Demand rate for the additional instances.
https://aws.amazon.com/ec2/pricing/reserved-instances/buyer/
At any instant in time when you lack enough reserved capacity to cover your running workload, you're billed for the excess.