The company owns the car but it gets used for non business purposes. (Including commuting to work)
If he had a company car or van used for business only then it would have no effect
If he had a company car or van that he can drive for personal journeys then that is a benefit
The key elements you have pointed out are ‘free lease’ (something that has value but is provided for free) and even the points that he earns for different levels
HMRC would see it as you having the benefit of use a vehicle.
(As it’s owned by the company / lease you also wouldn’t have the expense of servicing, maintenance, tyres etc)
Fuel is another matter - who buys it?
Does he or the company pay?
Does he account for private and business mileage?
Is there a travel claim made to pay him back for business mileage or a charge made for private mileage ?
HMRC will consider any private use elements to be a benefit, and will require income tax to be paid on the basis that it could have been paid as salary and therefore there would have be tax paid
Note that the recent court findings against Trumps businesses are for this sort of thing with undeclared personal benefits paid by company’s and the associated fraud / tax evasion