Unless the hosting provider adds in some custom plugins, there should be no difference in the actual installation of WordPress when using a cPanel 1-click option or uploading directly via FTP.
Once the site is installed, there is not really any more interaction with cPanel, other than being able to easily delete the database and files associated with the install.
If your client wishes to be the only person with access/ control of the site after build then ensure that only they have an administrator account in WordPress and only they have the details to login to the hosting, cPanel, FTP, etc.