Why is Apache sending duplicate Vary: Accept Encoding headers?

We put our Magento site on Sucuri and it is much slower than running it off our own server. Looking further, we notice that Apache is sending two Vary: Accept-Encoding headers and, as per Sucuri support, these duplicate headers are preventing the site from being cached properly by Sucuri CDN.

Here’s the curl output:

curl -IL https://domain.com
HTTP/1.1 200 OK
Server: nginx
Date: Mon, 26 Jun 2017 15:21:07 GMT
Content-Type: text/html; charset=UTF-8
Connection: keep-alive
Vary: Accept-Encoding |------> First header

Set-Cookie: frontend=fotji70ieh366b5k165u3mcd63; expires=Mon, 26-Jun-2017 16:22:19 GMT; Max-Age=3600; path=/; domain=domain.com; HttpOnly
Expires: Mon, 26 Jun 2017 18:22:19 GMT
Cache-Control: public, max-age=10800
Last-Modified: Wed, 14 Sep 2016 07:13:12 GMT
Set-Cookie: frontend_cid=sugOUAWt3WMknsbW; expires=Mon, 26-Jun-2017 16:22:19 GMT; Max-Age=3600; path=/; domain=domain.com; secure; httponly
X-Frame-Options: SAMEORIGIN
Strict-Transport-Security: max-age=31536000

Vary: Accept-Encoding,User-Agent |------> Second header
X-Content-Type-Options: nosniff
X-XSS-Protection: 1; mode=block
X-Sucuri-Cache: MISS
X-Sucuri-ID: 16007

I have gone nuts trying to figure out why these duplicate headers are occurring. I removed mod_deflate and mod_expires <IfModule> declarations from the Apache vhost and Magento’s .htaccess but the duplicate headers are still showing up.

I would greatly appreciate any pointers towards fixing this. Thanks in advance.