I'm confused. You can't not use it as a linked system, unless you activate the back first/only. There is no way to use just the front brake. Activating the front brake lever also activates the back brake. With the bike's substantial forward weight bias, and the weight transfer that occurs when you get on the front brakes . . . . adding back brake with the pedal increases the possibility of locking the rear tire and increasing tire wear. (yes, I know it ABS) When I first got the bike, I too activated both the pedal and lever. I soon realized the lever was all that was needed for normal riding. Pedal only for slow, tight maneuvers.
You still have to alter your braking habits when you go from one bike to another. The RT, ST13, and FJR are all the same style of bikes. And they all have different braking personalities. One does not fit all.