The price for the migration is calculated based on the Entity Limit.
Entity Limit is calculated based on the highest entity number among the count of products, orders, customers and blog posts. That means, with 1000 Entity Limit, you can migrate 1000 products and 1000 customers and 1000 orders and all categories and all other supported data types. So, if you only want to move 1000 products, the Entity Limit will still be 1000 and the price will stay the same.