If you need to log into the terminal as Root to edit an apache, php or ftp setting then you are doing it wrong. You are using a dumptruck to move a shovel load of soil around your flower garden.
It conflicts with the concept of least privileged. There is a lot loaded even in a text terminal, let alone an X GUI session, that does not require root. Having all that running with complete unquestioned access to your system is asking for trouble; malware, buggy software, user error.
Consider Webmin which will give you administrative GUI for your apache and such. https://localhost:10000 and your all set to quickly change around your settings. Ideally, learn the command line; apache config is fantastic by text tool. Your GUI tool is not remotely as fast as a quick vim/nano/grep edit.
In my case, I frequently use root requiring tools like nmap. I've always got a terminal open and su to root. But then, the command line is a happy place for me regardless of platform. It takes away the GUI abstraction and obstruction layers where not actually required.
I don't see the quote from the Mint site as user hostile but hostile against the overkill and security error that is "just log in as root". They are very correct by saying that even if one is absolutely sure they need to be logged in as root; they're 98% likely to be not doing something the right way.
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