They show this in the video! I actually almost wish the initial Steam Controller had these flat pads instead of the concave circles, it looks like it's going to be a straight up improvement.
I hope I'm wrong - I LOVE factorio and will definitely start a new save when the deck comes out. But even playing on my macbook touchpad, I wished I had a real mouse.
Of course, it's still just a computer at the end of the day. If you want to pair a Bluetooth mouse and play that way, that's your prerogative; I imagine that most people would be contented to use the touchpads out of convenience though.
A controller interface would have to break these macros up into layered directional menus. Nothing ground-breaking, but it is a different learning curve.