What you're seeing in the sequence is the keygrame selector, not whether or not it's operating.
The little box in the Timeline appears to indicate Bass is operating when it is not. If Bass if turned off in the Audio Mixer, I would have thought the Bass option in the Timeline should not be there. It is not operational, yet it is clearly there. Doesn't look right to me.
But, when you try to adjust the Bass level (by moving the yellow line) a little note pops up: "Bass off". So all is well and good.
It's there in the timeline because it's a keyframe selector, and that's all it is. Both Bypass and Boost can be keyframed individually in the timeline, so you need a way to select which keyframes you're seeing.