http://www.hmrc.gov.uk/manuals/eimanual/EIM31240.htm

That relates only to employees (and directors and other office holders
to be pernickety). Those restrictions for employees etc introduced in
FA 2001 did not apply to the self-employed. Have they changed that
position? If so, the relevant HMRC manual for them does not reflect the
change. Eg http://www.hmrc.gov.uk/manuals/bimmanual/BIM47701.htm
continues to show the use of mileage rates as optional.

Easy to get confused if you look only at the mileage rates - which are
often the better deal (especially for older vehicles).

--
Robin