I have trouble imagining that the gate scanner will catch this if you already have your boarding passes.

Imagine if the scanner beeped every time someone on a companion cert boarded before the paying customer, and the GA had to reconcile it....

Just doesn't seem likely to me.

Whether they could come after you later or not is another story, but I think it's generally agreed around here that the RPU doesn't get involved in one-off violations of ticket rules.