Rate limiting is (usually) done on a per-host basis. The only users who would be adversely affected are those who perform hundreds of requests per second from a single system.

Virtually every major website has per-host inbound request limits. This is completely standard practice and Archive.org is the odd one here.

And DDoS isn't the only concern. Legitimate users that run poorly written Python scripts that make insane numbers of requests can hog server resources, and rate limits with appropriate error messages linking to resources documenting efficient access patterns can improve the experience for everyone, and drastically cut costs for the service operators.