As you may have known, our automatic SSL certificates were only provisioned for sites that are served by Netlify and not proxied externally from Cloudflare, for example.
As of today, our system will automatically generate and renew SSL certificates for all sites, including those that are externally proxied
Newly added custom domains will have Let’s Encrypt certificates automatically provisioned 
Customers who already have custom certs but want one provisioned by us can click on the Use Let's Encrypt cerificate from the Domain management section of their site.
Customers who have custom domains that do not have a certificate because the site is behind an external proxy but want one provisioned by us can click on the Verify DNS configuration button from the Domain management section of their site to provision the cert.
Pro tip: We do not recommend proxying to Netlify for a number of reasons that are mentioned in our Why not proxy to Netlify? support guide.
As always, please let us know what you think about this update in the comments! 