1) If the AME isn't VAT registered the customer doesn't pay VAT (if it's a sideline to your main medical activities, which it is to quite a few AME's you'd have to work very hard to reach the VAT threshold each tax year).
2) If the AME is VAT registered, he can claim the VAT back.
This is another, albeit slightly different, aspect of this whole thing which also worries me greatly. Depending on their levels of activity different AME's will charge VAT, and others won't. If pilots shop around for the cheapest rates (how many of you do ? ) then loyalties to the smaller, non VAT registered, practices might increase, to the eventual disadvantage of the larger VAT registered practices. How fair is that ?