The Warren Haynes Mod is just cutting the bright cap. Or throwing it on a switch instead of having it hard-wired. Cutting this cap shouldn't do anything to change how the controls work. If you want to have some fun, throw a bunch of cap values on a switch. One cap for on/off, or two caps for three flavors, or multiple caps on a rotary switch and go nuts.
EDIT: I should point out that with bright caps on all amps (like Marshalls), they become less effective as you turn the gain up. So really, the control is already "variable" in stock form. Removing the bright cap (the mod) doesn't change how any of the controls interact or work though.