Yes, you're correct: by using multiple -d switches, you'll get one certificate with multiple domains. I believe the first -d switch will be the CommonName (CN) domain. And all domains are added to the SAN list. But even so, if you've hit the rate limit, that limit doesn't suddenly vanish
Perhaps you can experiment first by using the --server https://acme-staging.api.letsencrypt.org/directory
option. That way you can try the client and receive certificates (which won't work online, 'cause they'll be signed by some "Happy hacker" CA in stead of Let's Encrypt Intermediate X1) and the staging server doesn't have such strict rate limits.