Does a Sub Panel have to follow Article 230.79? Or can you configure it however you want? I ask because I am wondering if since it is a panel if it is considered a service and since it would have 6 breakers if it would have to follow 230.79(D) for amperage.
The 6 breaker, or more generally, 6 disconnect rule, refers to 6 service disconnects. Once you're considering a location that is load-side of a service disconnect, you may have as many breakers/disconnects as works best for you. Subpanels can be filled with as many branch breakers as the manufacturer allows.
You still consider total calculated load for the subpanel, just as you would for the main panel. You follow a similar algorithm for "adding up" the total connected load to a subpanel, as you would for a service, but limited to the scope of the loads served by the subpanel. Any rule specific to "service conductors" would not apply, since the feeder to the subpanel doesn't count as service conductors.
Subpanels are usually fed from branch breakers of main panels, so the branch breaker ultimately limits current to prevent overloading, even if you do turn everything on at once, against all odds. The purpose of the load calculation is to determine how large the subpanel and feeder need to be, in order to handle the statistically likely total connected load, and make it unlikely that you nuisance trip its feeder breaker. Accounting for load diversity and likely user behavior, to keep the sizing within reason.