In there said CNAME flattening works if CNAME record is grey clouded.
https://support.cloudflare.com/hc/en-us/articles/200169056-Understand-and-configure-CNAME-Flattening
But in there said SSL works if CNAMEr record is orange clouded.
https://support.cloudflare.com/hc/en-us/articles/200170566-Why-isn-t-SSL-working-for-my-site-
Is there any way to use CNAME flattening(root domain with CNAME) with SSL certificate?
I have an orange-clouded flattened CNAME subdomain working with SSL. I don’t see why it wouldn’t work for the root domain. Is something not working?
If I make it orange-clouded, is it cause problems receiving email?
Only if your MX record points to it.
No, that will be fine pointing to zoho. You can leave the CNAME set to 
.
No, that’ll work since it’s pointing to zoho.
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