People who use PayPal Advance know that the import from paypal shows these payments as purchases. These payments are on every transaction and can result in hundreds of purchase entries with the wrong VAT applied.
If they were assigned to a purchase code (paypal advance) for instance, the VAT setting already set in that purchase code could override the paypal setting.
I don't see this being too difficult to implement as the field is already there, and the time it would save from manually changing hundreds of imports would have huge benefits.