I haven't got a clue why the RAF still use QFE either but it works. QNH also works. IMO it does not really matter what system you are using as long as you understand it.
I use QFE for take off and landing. I can understand the reasons for using QNH for take off but switching like that would confuse the hell out of me. What if you are doing circuits? Do you change the setting downwind? Do you change back again during the touch and go?
If you don't like QFE then don't use it. Simple. It has it's advantages but it's not for everyone. I frequently fly to civilian airfields where QNH is used but it is not a problem. Simply ask for the QFE.
IO540
I am pretty sure I know which units used the Skyforce GPS and if you do then you'd know they are extremely highly respected. If yours is no good then maybe there is a problem with the operator. True, it is not the best kit in the world but it does do what it says on the tin.
Why so Anti RAF anyway? Did they turn you down?