In my view, any necessary labor that was exhausted in order to build the finished product or provide a service deliverable would be chargeable to that project as a direct expense. The test would be, would an employee perform the questionable task if it were not for the product being produced? If the answer is no, then it should be a direct expense to the ...
Risk management approaches
As any risk, you might have four ways to address them:
Based on your situation, you invest a considerable amount of efforts on reduce them as much as possible. Thing is, maybe they can't be reduced any further and thus, you need to explore other approaches.
What else to do?...
From your text I assume that:
You mostly have issues with small scope / minor customization, which your customer keeps demanding from you to do for free.
Your typical delivery tactics is to deliver the first project with fixed scope / fixed price, and then sell time-and-material consultancy services on top. You want to determine which scope belongs where.
Communication is key. At times, you might need to over-communicate to keep your stakeholders in sync. Creating rapport and building trust takes its own sweet time.
As a service provider, the number of features you deliver or the number of tickets you close will be your currency. Defining your invoice cycle with your SPOC will hasten the sign-off process.