The WN software flags this when they close out a flight (when the agent is done scanning all tickets in).
I have seen WN charge someone in this situation for a last minute walk up ticket. The alternatives was to wait for the next flight if the companion
would make it to the airport in time. They paid.
If a situation arises that the companion and earner gets split up BY WN for WN's benefit, and they have the reservations noted accordingly, then nothing happens. I volunteer when overbooked often and sometimes they only need one seat, not two.