The rate that HMRC allow is irrelevant to business mileage charges, it is merely the rate that a company can pay its employees for use of their private vehicle without the monies becoming a "benefit in kind" as classed by HMRC with respect to income tax.
The HMRC rate will only come into effect if you are employed by your company and use your own private vehicle for business use, in which case it will also have to be insured for business use.
If you are self-employed then you can't really claim 40p per mile from yourself can you!
Your vehicle would be a business overhead, thus the insurance, fuel etc. would all be offset against your profits etc. with regard to taxation.
As a business you can charge your clients whatever you like.
If you are employed by your "own" limited company then I would expect the vehicle, insurance, fuel, etc to be paid for by the company, thus there is no personal benefit to you, so as long as your books are in order, there is no relationship between the HMRC rate & what the company claims, or charges as the company does not pay income tax.
I currently charge 50p per mile for the van, fuel, vehicle insurance etc. travel time is at my normal hourly rate on top of this.