Reality is not flat, so why are our digital interfaces?
Minimalistic, flat design removes what's familiar, relatable, and disconnects us from our natural world.
Another partial reason designers chose to make GUI objects dimensional is because everything in the real world is dimensional. Calling digital squares that perform an action “buttons” is because they were similar to a physical button or switch—it depresses when you push on it. It’s interesting Material Design elevates the button when you push on it. Certainly it’s counter intuitive, but if there’s not a large cognitive dissonance, then it’s okay.
In the end, if your design is crafted around the purpose of the interaction, then you can leverage that tiny moment on interactivity as a way to connect with the user in a visual and delightful way. Strong communication is strong design.