Not defending Waymo, but you're supposed to open the trunk either using the button on the touch screen in the car, or the button in the app. They tell you do do this in the app. If you open it this way when getting in, it'll automatically open at your destination too.
As far as I know, the button on the back of the car itself isn't integrated with their computer system for whatever reason.
Also keep the passenger door open until you've got everything. I do the same thing with taxis and Ubers too.