but I find it hard to believe the cost of issuing a license plus 6% could possibly be as high as it currently is for PPL/ CPL
You are quite right but items are not costed in that way. The CAA charge for some services and they have numerous functions that generate no income at all so the services they charge for are invariably well above the actual cost of producing those services. The 6% is what they have to pay the government.
According to stats in the latest edition of FTN, for the two months to 31 May 2010 the UK CAA generated a profit of £392,000, compared to a budgeted loss of £321,000.
With a turnover of around £70M thats less than .5% profit!