My ATPL course was about 50/50 between grads and non-grads and it made no difference at all to the results of the groundschool or flying. Only 3 of the course had any theory resits to do, and 2 of them were grads. If anything, the grads with backgrounds in physics or engineering found the groundschool hardest as some of the more technical subjects were very over-simplified in relation to their level of knowledge and they found it hard to accept the JAA answer to questions which they knew were technically incorect.
More importantly, holding a degree has made no difference whatsoever to employability after the course finished - it is again about 50/50 between grads and non-grads. Sheer good fortune appears to have played a bigger role in chasing down the elusive vacancies than anything else.