When you use a paper boarding pass, you hand it over to the agent to scan. An agent can easily glance and see your boarding group - at that time, they at least have the option to send you back and wait for your group.
When you use a mobile boarding pass, the agents never really look at them - you scan it yourself at the gate. All that happens on the screen is your assigned seat turns from yellow to green. There is no indication of your boarding group. I've never had an agent look at my mobile boarding pass to confirm that I'm boarding with the correct group.