Hello,
1.
It looks like CloudFlare may have been caching the cPanel redirect. I temporarily stopped Apache to force CloudFlare to update which page it loads when you access /cpanel and after clearing my browser cache I am no longer being redirected to the cPanel login page when loading
"http://site.com/cpanel."
I have attached screenshots of what I am seeing on my end. Could you try clearing your browser cache and or using an alternate browser that has not visted the above URL to see if you are still being redirected. If you are still being redirected please try enabling CloudFlare's developer mode which disabled caching and see if that resolves your issue.
Regards,
--
Michael B.
Linux Technical Analyst
cPanel, Inc.
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2.
There are no rewrites to handle the "/whm" script alias match in Apache's configuration and I'm not able to replicate the page still redirecting to WHM's login page as seen in my provided screenshot:
=====
# grep -i scriptalias !$
grep -i scriptalias /etc/apache2/conf/httpd.conf
ScriptAlias /cgi-sys /usr/local/cpanel/cgi-sys/
ScriptAlias /mailman /usr/local/cpanel/3rdparty/mailman/cgi-bin/
=====
I suspect you are still cached in some way on your end. Could you try loading the WHM URL on another device?
3.
I would recommend keeping the "/cgi-sys" script alias match as that directory contains a number of cPanel CGI scripts such as the suspended account page and the default error page for misconfigured domains.