So, I still think they would be okay, not hidden, if you emphasized them a bit more. As I said before, make them bigger while doing a roll animation and let the player understand the significance of that and anticipate the outcome. I think that would be better; right now, they just felt like an afterthought to me.
In terms of things you could do to ease them into the background, my first thought would be some system tied to the theme on the surface. You could call it something like the "Bravery" system and explain it away as something like "Only 2-3 characters per turn will be able to summon the willpower to take action against the cosmic horrors they face per turn; make your choices wisely." You could probably come up with a more creative name and reasoning, but it would be easy to put it in as a hidden system at that point if you wanted to go that route. But of course, you would need a new name then, just spitballing design ideas. :)