Correct Bob. Any white battery should be properly discarded. Like you, I am a huge fan of the PS2 3 volt boards. You have always done it right.
I have done a good number of Williams Genesis engines to PS3. One very useful thing using the LED lighting is if you need a red light, do the following. Get yourself a fresh red Sharpie and color the LED. They show a great red color and no worry about heat burning the color off.