Huh.
I never saw that before. I have ultegra and XT pistons, which I think are ceramic. (Not sure about that, either.)
The way I use them is to leave the pads in and I jam it in between the pads.
I used to do it with a broad screwdriver, but that was more likely to scratch the pad surface.
I wouldn't apply the tool directly to the pistons. Even with a plastic tire lever, you have to be really careful. I keep old pads so I can indirectly press on the pistons through them.