Hey, I use Hestia Control Panel on a VPS to manage my hosts.
The Domain Is: pivotpixels.com
I have SSL issues with it.
For the main website (currently a default Wordpress install), HestiaCP dashboard domain and mail server domain. I have installed Cloudflare SSL in control panel.
But in browser the certificate is still showing Let’s Encrypt E1 certificate
In Cloudflare Settings I have the settings to Full (strict)
You are not going to see the Cloudflare origin certificate when you visit your site while it is 
proxied through Cloudflare. You don’t want it to be presented to your visitors because it will throw an “Unknown Issuer” warning. It is signed by Cloudflare’s own private certificate authority and is used to encrypt the traffic between your origin server and Cloudflare. The certificate your visitors see is automatically generated by Cloudflare and may include a certificate from the Let’s Encrypt certificate authority, as it is among the issuing CAs that Cloudflare uses.
If you want to test your origin certificate, you can either pause Cloudflare from your dashboard, or set the relevant DNS entry to 
DNS Only to see if your origin server is presenting the Cloudflare Origin certificate.
Okay, So I’ve figured it out for the most part.
If I keep it proxied, visitors will see a Let’s encrypt SSL but what’s actually happening is the visitors are encrypted to Cloudflare with Let’s Encrypt and then it uses Cloudflare server to encrypt connection between my server and Cloudflare server.
If I keep it without proxy. My visitors will see the Cloudflare ssl. but will get untrusted SSL warning.
So far everything checks out.
Last thing, is there any way to show the Cloudflare certificate to the end user without getting untrusted error? (Asking as I’ve seen a lot of website with Cloudflare origin server and they work fine)
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