You can accept payments as a non-registered charity, in the UK at least. Not sure how it works internationally.

https://www.paypal.com/uk/webapps/mpp/not-for-profit-2

The problem is that PayPal’s rules are vague and opaque, and they apply them arbitrarily. You have no real recourse to complain about one of their decisions. I can maybe see how it’s painful for GitHub to deal with them.