I am a having a little trouble understanding the difference between running the terminal emulator from the GUI (gnome) and booting straight into the terminal. I have been a system/network administrator for a little over 10 years and I am very familiar with terminal emulation and how it works on a Windows platform, however I was told by a Linux "engineer" that running the terminal emulator from the GUI (as root) would not grant the proper permissions to edit the kernel source code. He said you need to boot to the console and login as root.
Booting straight into the terminal means running in the text console. Technically, this console (/dev/console, /dev/tty1, /dev/tty2 and the likes) is just provided by another terminal emulator.
Real terminals like the famous VT100 used to be connected to computer through serial lines but are now essentially history.
About the kernel editing restriction, I guess you misunderstood what was told by the Linux engineer. Obviously, nothing prevents you to edit a file whatever the terminal emulator used. However, if you want to see console messages while experimenting with a custom kernel, that makes more sense.