As I understand it, the MoD have insisted that a crucial part of the training at Bournemouth isn't completed, such that it doesn't compromise what the RAF wants but does preclude the pilots from getting ATPL A at the end.
Such short-sighted petty-mindedness is why so many have left over the years - if they guaranteed ATPL A or H at the end of Service then far fewer would leave for fear of being left behind.