This is also a huge problem for my shop and my accountant is always getting frustrated with this system.
We are a high volume / high dollar value store. Tax reporting on partial refunds (with restocking fees) is also a pain for us, as we are trying to use the Shopify finance report for our bookkeeping. Tracking this externally is not a good solution as my accountant has to spend time sifting through the orders to find the amounts and break them out themselves on quickbooks. Which every month leads to continued frustrations on both ends.
We would very much like to see accurate tax reports that would pass CRA / IRS scrutiny. Handling tax amounts on partial refunds is a must for this platform.