I understand the desire to want to have the option for a full 1000ma for each LED. But be careful. You'll still need something to limit the current to that for each LED. The potentiometers won't be enough. On a potentiometer's highest setting there is almost no resistance. If you run an LED off that with nothing else to limit the current, you will blow your expensive LED.
But they are right on the color mixing. The only time you'll get to a full 3A is if you are running red, green, and blue at the full 1000ma. Red is most likely going to be pulled down abit anyway, unless you are a pink kinda guy.
I honestly think you'd be better off running all three together off a single 1A source, and potentiometers off that. The single colors will be at their brightest, and the mixes will be about the same brightness. The other way, you'll end up with really bright mixes and standard single colors. I'd go for equal intensity if I were you. Then you won't have to worry about heat or low battery life.