I don't think there is a bulk discount but prices vary by tld.

Base rate for a .com is around $8 plus a small icann fee. If anyone is selling it for .99, they are simply eating the cost in order to earn a long term customer.

In this case with cloudflare, I'm sure the point is, like their other products, to offer the free service as a gateway drug to their profitable enterprise products. They have an Enterprise registrar service that is pretty pricey.