I used dehydrated to get a letsencrypt cert for 'gimp.ca' but the alternate 'www.gimp.ca' didn't get into the cert for some reason. My domains.txt was just "gimp.ca www.gimp.ca" so I'm not sure what went wrong.
I can't help, I always used certbot for my Let's Encrypt (and never had any problem getting a multi-domain cert). With certbot, just running certbot certonly --webroot -w /some/path/to/www/ -d gimp.ca -d www.gimp.ca (then regularly in a cron to update the cert automatically) would be working fine.
In any case, for us, it's not a problem. We can just use the gimp.ca domain. It's fine.