As far as I know, if you issue one cert including SANS for:
Regarding rate limits... it will count as 1 cert for
domain1.tld AND 1 cert for
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.