If my limited understanding is correct, you would get transferable civilian pilot qualifications as part of your Pilot certification through the RAF.
Now, something to bare in mind is that a pilot positions in the armed forces are extremely competitive. I don't know specifically for the RAF but I know for the Royal Navy that (as of about a month ago), they had 700/800 pilot candidates lined up to do the Admiralty Interview Board, competing against 6 or 7 pilot vacancies. So be realistic about the chances but give it a shot by all means.