If Wagner had been scored differently at US Nationals and had made the Olympic team, and had she placed 15th or higher at the Olympics, she would have been at least Top 24 WS. She didn't skate well enough at US Nationals to leave any doubt that she had earned a spot outright, she was scored the way she was, and there was no body of work argument for her.
Wagner knows what happens to her body over the course of a season, and, yes, she's organized her season around that. Maybe she did the math and knew where her SB and WS would likely land after the general historical upward trend of championship and Olympics scores, or maybe she was taken by surprise. (I don't have a snapshot of the SB and WS lists at the time to be able to assess whether it should have been a surprise.) The Euros and 4C's rosters were available by US Nats and the post-Euros WS points, available soon after, would have been a good indication, since Olympics and Worlds points can be only incremental, with one championship/season counting.
She may also have been considering whether or not she would continue skating or have had more pressing issues in her life than whether she'd be selected for GP in 2018-19.