I think that the benefit-in-kind issue is covered by this piece of legislation.
http://www.legislation.hmso.gov.uk/a...3/30001--z.htm
The summary I take from it is that if the costs of training are solely the costs of providing work-related training, including the use of a company asset to provide that training, then there is no taxable benefit.
By paying for 'pleasure, or 'own use', and as long as you are strictly honest about how you do it, then this legislation can be interpreted as covering commercial training. It would be reasonable to interpret the legislation such that if you were to limit the recovery to only those flights where an instructor was present, or specifically directed as required by an instructor, or the costs of relevant exams and training courses, then it should not be considered as a benefit in kind!
BW