Thank you for the report:

1. Could please specify exact places where you are experience these problems >

2. We can't add it as a setting to mix since this isn't system feature, but a setting in a module, however I believe that you can change colour and transparency for each tone in duotone icons via custom styles in particular mix:

https://fontawesome.com/how-to-use/on-the-web/styling/duotone-icons