Disagreement re sole trader

Have a sole trader who is vat registered.

Has a company van used 100% business.  To keep the mileage on the van down, and in line with the contract he uses his car as well for business.

Car is on a HP.  If we put the car through the business can you choose to:

A. put petrol re car to drawings and claim vat back on the mileage only rate. (i have made sure he keeps a mileage log)

B. fuel through business and claim vat back and have a fuel scale charge.

I say you have a choice, and once made you have to stick with it.. A N other is saying as Vat reg, it has to be option B.

Can anyone confirm.