If any product lies under various categories on which the admin has set the commission, then, in this case, the highest commission will apply to the product.
Also with Magento 2 Marketplace Advanced Commission module gives the ability to the admin to set commissions for products, categories, and seller categories.
Please follow the user guide for more information on Magento 2-Marketplace-Advance-Commission
Please do contact us for any further queries or requirements. You can also check our Magento 2 Extensions for additional features.