Pay to play.
If 500 Startups funds a company ($50,000) to join the accelerator, it will charge fees to help cover the costs of running the accelerator office space.
(I think part of the reason is that some startups have more team members, which takes up more resources in the office.)
I don't care if psychologically $35k sounds better than $50k minus expenses to you. It makes for better founders and better companies. You should think about it from this perspective.
Can you explain this part a little more?