This seems to be an issue with commerce pro in general and not specific (Although it was discovered on one of our apps).
When you have commerce pro with multiple stores, you can add items to your cart from as many of those stores as you like, however delivery will only be calculated based on the distance of the first store.
This would need to be changed so you can only add items from one store at a time (the same way uber eats etc work).
Based on your current setting, it might be using setting from Default Store.
Please select list view as Store List- this view allows individual store settings to be used while placing order.
Just for clarification, are you referring to CommercePro with multiple stores or are you referring to CommercePro with Marketplace?