Following the suggestions of https://www.netlify.com/blog/2017/02/28/to-www-or-not-www/ - I created a site with a custom domain only for the www subdomain. But, as mentioned in Netlify takes control over the root domain when using www? , Netlify tries to takes control of the root domain and does not proceed in creating the Let’s encrypt cert (probably because it never finds the root domain at netlify).
My DNS and root domain are hosted elsewhere. It looks in Netlify takes control over the root domain when using www? people like @luke have a special switch to fix this. Is it the way to solve this?