Hello @My1,
As far as I know, if you issue one cert including SANS for:
domain1.tld sub.domain1.tld domain2.tld sub.domain2.tld sub.sub.domain2.tld
Regarding rate limits… it will count as 1 cert for domain1.tld AND 1 cert for domain2.tld.
So, you only have issued 1 valid cert for 5 domains/subdomains (2 for domain1.tld and 3 for domain2.tld) but you could only issue 4 more certs for domain1.tld and 4 more certs for domain2.tld in next 7 days.
Thats what I understand regarding rate limits, maybe an official explanation on Rate Limits for Let’s Encrypt topic should be a good idea.
Cheers,
sahsanu