Correct, any changes to your itinerary made in person or by phone will be reflected on the conductor's iPhone, unless maybe you made the change 2 minutes before boarding and the train was in an area with no cellular data to allow the conductor's phone to know about the changes.

You'll also only get one QR code per reservation, without regard to how many segments your reservation may have nor how many people are on said reservation.

And if you now try to board an earlier train than the one you're supposed to be on, the conductor's iPhone will inform him that you are on the wrong train. I'm not sure what, if any, latitude the conductor has to override things and allow you to remain on the train.