Thats very strange. I was under the impression that a Part-FCL licence entitles you to fly Annex 2 aircraft.
From
http://www.caa.co.uk/docs/2330/g-May2012_v6.pdf 1.5
1.5 The 2012 amendment of the Air navigation Order renders EASA licences with the appropriate class rating to be valid for UK-registered non-EASA aircraft within those classes; thereby avoiding the need for the holder of an EASA PPL(A) with SEP rating to also hold a national licence in order to fly an amateur-built aeroplane or a Tigermoth, for example...
The exception is for type ratings, as you can't add a type rating for a non-EASA aircraft to a Part-FCL licence so you need the piggyback national licence...
Also see
http://www.caa.co.uk/docs/2330/h-FAQs%20May%202012.pdf part 39.
How are they justifying the extra charge?
I'm sure there are more up to date references that someone else can find (I've not got into the ANO / Cap...