Just speaking from my own experience as an IB student applying for PPE this year, I didn't find it to somehow disadvantage me at all - probably the inverse if anything.
At interview, the tutors seemed fairly familiar with the course etc, and aside from unfamiliarity I can't see any real reason to disadvantage IBers. Given the increasing popularity of the course, I can't imagine there are any/many interviewers who wouldn't have a clue about it.
Some people moan about comparatively high IB offers, but imo 38-40 points is entirely reasonable.