The Boulder ACME differences: boulder/docs/acme-divergences.md at main · letsencrypt/boulder · GitHub found from here: Documentation - Let's Encrypt
says about the Retry-After header (emphasis mine):
Section 6.6
For all rate-limits, Boulder includes a Link header to additional documentation on rate-limiting. Only rate-limits on duplicate certificates and certificates per registered domain are accompanied by a Retry-After header.
The new Rate Limit page: Rate Limits - Let's Encrypt
We include a Retry-After header in all rate limit error responses, indicating the duration your client should wait before retrying.