Why do people think questions about cPanel/WHM is the same as
questions about cPanel?
Umm, we don't.
Forget all of your points about contacting vendor support for a moment, and examine the key piece of why cPanel questions (and the vast majority of other GUI control panel questions) are off-topic here. This is from the close reason that was (appropriately) chosen for your question:
Questions involving web hosting control panels are off-topic at Server
Fault because they customize their systems such that normal
administration tools and methods no longer apply...
Period. Full stop. Do not pass go, do not collect $100. cPanel messes up a server to such an extreme extent that standard sysadmin practices, tools, troubleshooting techniques no longer work. A symptom of this issue is even mentioned in your own question:
I am able to secure with an A rating using the details below, but
cPanel services doesn't allow the level of flexibility in the
protocols which would eliminate the problem.
Don't use a product that hampers you from doing your job. If you're required to use it for your job, and the software is not doing what it needs to do, then issue a feature request with the vendor.
Yes, moderators rush through a lot, but they sometimes miss the key
element of moderating --- TO READ THROUGH BEFORE making any judgement.
I recently made a post regarding the administrative side of
cPanel/WHM, which unfortunately bears the same name as the user
control panel 'cPanel' which is what is being confused here.
There's no confusion here, either due to not reading your question nor due to conflating cPanel with cPanel/WHM.
The server portion, is not unlike managing a windows server, but in
Linux, with full shell access and control at 'root' of everything, and
it happens to have a web-gui to assist in administration of some of
That's a poor analogy. Windows server management tools are native to the system, designed by the same company that built the operating system. As such, they're extremely well-tested, highly-integrated, and well-supported. (I'll take this opportunity to mention that even the likes of Microsoft have seen the light with regards to the pitfalls of relying too much on a GUI for server management, as more and more Windows Server management is shifting over to text-based technologies like Powershell, WinRM, and even SSH). cPanel/WHM, on the other hand, is an attempt to bolt a GUI on top of an operating system that is designed to be managed using nothing other than an SSH client.
So why choose to exclude cPanel -- arguably the #1 control panel for
hosts to install...
Just because a software is popular doesn't give it a free pass here. We're not excluding cPanel (see my below "As an aside" comment).
I understand - you asked a question, hoping for an answer. The question got closed, which hurts a bit. The fact remains that the community is very strongly against accepting cPanel questions, and has spoken time and time again on the topic, always with the same outcome.
So, where to go from here: not to beat a dead horse, but call up cPanel support. Honestly. You're paying them for their software and support, so take advantage of it. They'll be able to help you better than anyone here can.
As an aside, we very rarely close questions due to someone not contacting vendor support before coming here. Very rarely. Your question was not closed because you didn't go through cPanel support. It was closed because the mere presence of cPanel on a server makes troubleshooting this sort of thing difficult if not impossible to do without causing the entire cPanel house of cards to fall down around you.