Hello @AMejia9,
We had done something like this when we have added a few products automatically when a deal is created. That is something you can also do using custom workflow action.
You can create a deal-based workflow and based on the conditions when the custom workflow action will execute, you can add the calculated fee.
Alternatively, as the Quotes API is also available in beta now, you can use those APIs to achieve this functionality. But, as I said they are in beta for now - Accounts Dashboard | HubSpot
Also, we have experience and worked on similar customer app development, you can always connect us and our team will help you out with development and implementation. 
Regards,