Kenneth - form AP1 is the application form. Form AS1 is the legal deed by which an executor transfers the ownership to a beneficiary. The two go together but only form AP1 then applies to register form AS1 hence only it refers to the fee aspect
I can understand the confusion caused if you/she felt two fees were payable
Scale 2 fees - payable just once for the single application -
HM Land Registry: Registration Services fees - GOV.UK
An application would consist of the form AP1, AS1 (transfer), copy probate and forms ID1/ID3 as appropriate to verify the identity of each party.
I hope that helps iron out the confusion