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 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?
(I think part of the reason is that some startups have more team members, which takes up more resources in the office.)