I have a client that wants to claim mileage allowance on SA return but I found that the mileage was claimed on every sales invoice that she issued. It is also paid at a higher rate than HMRC's allowance.
I feel that she is not entitled to claim this allowance, but may claim on capital allowances for the vehicle itself.
I would suggest that the client can charge their customers whatever they see fit, as long as the customer agrees to it. In my opinion they can still claim the 40p per mile etc on their SA.
If it makes you feel better why not ask your client to call the mileage on their invoice something else, but I really don't see the need.
The views expressed in this post are my own personal (HRA protected) views, and are not representative of any organisation I have any involvement with.