I tried and: it works on dotted and undotted notes. If you click on a (invisible) note that has the opacity already set to 0% the little square is not visible: the little square near the Color switch seems to show exactly the color and opacity that you have set up: if the opacity is 0% than you don’t see it (but can click on it because it always exists) If you switch the switch off and on again, the color settings will be resetted to black, and appears black again.
This was already been requested: