I have set the main icon to fade when I'm supposed to wait before using the ability. But I find my self very often using the ability too early. Is there a way instead of fading the icon, completely hide it? I wasn't sure if this was the right place to ask this so sorry about that

No, not at this time. I am working on tweaking it so it visually looks more like when you're lacking resources, but you still have the timer or icon indicator options (in display settings) until then.