Unofficial Skyrim Special Edition Patch

To quote UESP: "Because these perks affect the item itself, it will also benefit other secondary enchantments (such as those from having the Extra Effect perk) on the item that are not related to elemental damage. For instance, an item with Fire Damage and Absorb Health as its enchantments, when used by an actor with Augmented Flames, will also see a +50% increase in the effectiveness of the Absorb Health effect."

This effect is also present on Stalhrim weapons that have an innate effect bonus with frost enchantments: "When multiple effects are enchanted onto a Stalhrim weapon(via the Extra Effect perk), if one of the effects is Frost or Chaos Damage, any other Destruction effect will also be increased in effectiveness, even if it is not itself Frost-related. For example, a 32 point Drain Magicka effect will be boosted to 40 points when paired with any sort of frost damage effect, even a single point. This effect does not occur with armor."