AWS Marketplace costs are not taken into consideration while processing partner Billing Rules or Custom Price Books typically but some Marketplace charges such as Bedrock will be factored into Percentage of Spend, and AWS Support Billing Rules.
Marketplace charges are passed to the end customer and also not included in calculations outside of Bedrock related charges for Percentage of Spend, and AWS Support billing rules. Custom Pricebooks won't consider Marketplace charges in any regard.