Usage and in-game effects
"Auto calc stats" is a setting that allows an NPC's statistics to be directly or indirectly drawn from their class. For example, if it is checked for an NPC in Fallout 3 who is set to the VaultDweller class, that NPC will then receive the SPECIAL "5,5,4,5,5,5,5" and the tag skills Science, Unarmed, and Small Guns. Each class gives a different set of these skills.
If "Auto calc stats" is not checked, then an NPC's skills will not be affected by their class. Conversely, if an NPC levels with the player, then they will draw their stats from their class. This is because setting an NPC to level with the player automatically checks "Auto calc stats."