Gifting point multipliers function in a Post Checkin Campaign is processed as a gift. Points gifting is a different function than earning so any earning exclusions for the business are not taken into account. This gifting will apply to the sum of all items on the check.
The only guaranteed way to prevent gifting points on excluded items is to add the same exclusions to the Line Item Filter built into the Qualification Criteria for the Points Multiplication Campaign as seen below. 