The opacity slider is not a level control. The level controls are the red, green and blue knobs for each channel (turn them all down if you want to null your input.) The opacity control is like a transition between additive and alpha channel blending. With opacity at zero, everything is additive (like a normal matrix mixer.) That is, layered inputs will stack on top of each other, each one adding to the brightness of the channel. With opacity at 100%, the related input mono source is subtracted from the lower channel mono sources before a 0V clipping circuit that is between the mono input and the RGB gain controls. It’s a bit of analog math to allow you to segment and transpose shapes before colorization.
So think of Color Chords like an odd duck sitting somewhere between a colorizer, matrix mixer, and analog computing functions. It’s meant to be fed a bunch of overlapping patterns and shapes. Marble Index is what you want, if you want a full RGB compositing environment with voltage controlled opacity and masking.