can you get a second certificate? i'm not sure how the technology works, but since let's encrypt is free i think it could also be automated to solve this problem
Certificate authorities charge extra for it, of course they do. DigiCert brands this as "Multi-Domain (SAN) Certificate" and charges nearly $300/yr, while my choice provider, sslmate.com offers the same for $25/yr.
And now $0 certificates with Let's Encrypt, I'm sad to see sslmate.com's business hurt, as they are the first to provide no-bullshit sysadmin-focused CLI tools to get the job done. I'm very wishful to see DigiCert.com and others like it go bankrupt, however.