Ok. The difference is that Grub Customizer runs directly as root. The alternative way is that it creates a root instance by running `pkexec [...]/grub-customizer`
The error now means that Grub Customizer didn't find the specified pathes. Please check the debug output starting with "checking for". Ignore the BURG checks (this is an alternative bootloader) but look for the parts of grub. If there aren't errors but messages like "not found", you have to configure the file /etc/grub-customizer/grub.cfg properly.
Yes, fedora 16 uses Grub2 as default.