I know Fantastico has the ability to install WordPress without the need of FTP or database credentials but does it carry the same limitations?

Thankfully, no it does not. I installed one of my WordPress sites with Fantastico, and you could do anything you want just as with a normal install. Since then I have setup several installs the manual way, which as you say was easy for someone like me who is tech oriented. My host now uses Softaculous instead of Fantastico, and it also allows updates, custom code, etc. Its even integrated with cPanel to give you a notice there when an install is out of date.