You have to remember that Mil accreditation was originally obtained as a recruiting and retention incentive. Join, give HM some of the best years of your life, then (if you want to) leave and join the people-tube world with minimal faff.
Whilst some might wonder why the RAF might still need such a thing, they should perhaps note that most industry observers are of the opinion that airline recruiting has at last started to pick up. If the RAF is to compete with the airlines for new pilots (and the RAF is probably more in need of a stable demography than the airlines are), this valuable incentive simply must be protected. Otherwise potential recruits might well wonder why they should ever bother with the RAF, if their service ends up being worth jack $hit towards an airline job - particularly when airline pay is based on seniority and time served, rather than on competitive standards. 'A' cat or 'C' cat, CR(S) or CR (or whatever the latest incarnation currently is) simply doesn't exist in the airline world - whoever has been in the longest gets the captaincy opportunity. So why compromise that by spending 15 years in HM's flying club if there's no ultimate reward?
I do hope that someone in Learning Command pulls their finger out sharpish - otherwise no pilot in the ME world is likely to hang around much longer, from what I hear.