Look at page 57 of the report. They reproduced various situations in the sim and photographed what the displays look like.
It makes more sense now. Like the accident FO and many of us here, I've flown both Boeings and Airbuses of this era. And, in the heat of battle I've certainly botched an approach or two. I've always been able to catch the error and fix it or go around.
The FO had also flown 767's and B-744's from her type ratings and the factual report. On many FMS's in those planes the waypoints will automatically sequence if you don't extend off the final approach fix. Also, you get path guidance that you can chase with V/S even if you forget to reset minimums in the MCP altitude window prior to the FAF.
Putting the MDA in the approach page tells the box when to disconnect the autopilot (50 ft below the MDA). Also, until you've entered the numbers, there are no cues in the box to allow you to activate the approach. I didn't see anything in the cvr that suggested they put anything other than 1200 in there.
The question of what would you put in the approach page MDA box was asked repeatedly in the pilot interviews. From what you say it wouldn't matter if the path is never captured in Profile, the box would never see the entered value to disconnect the autopilot.
Thanks again.