It seems like this could be solved with a simple programming fix. The scanner should give an error when a boarding pass is scanned more than 5 positions early (i.e. if A20 just scanned the boarding pass, anyone with A25 or later won't scan). Even if the GA is given an easy override (as they would need to because occasionally there might just be 5 people who aren't at the gate), it gives them an out to not feel like they're being rude when they say to the person that they need to board in position. The person will hear the error sound and it's the computer that's telling them to wait rather than the GA.
I'm guessing that since this hasn't been implemented, it's not just rogue GAs failing to enforce policy, but that WN itself doesn't care if you board in order.