I've seen this happen before ... it's about prize money. Suppose they made final 40 in A division of Pinburgh. But for whatever reason (poor planning or emergency) they need to leave Saturday morning. By checking in and leaving, they are assuming they will get 40th place, and still the $300 prize money. If the don't show, they get nothing.
Now is that really the case? I'm not sure what the rules say. But they know for a fact that leaving will give them 0. So they at least try, and see what happens.
At NWPAS, due to the difficulty of filling in spots the next morning (not an obvious "who is next in line" based on qualifying), we don't take any alternates. If someone doesn't show up, 1st game they play is scored as a 4-player game, so maybe a freebie point for players in that group, but not really if you consider the player could have shown up and gotten last place. If player is a no-show by 2nd game in the round, the group plays the rest using 3-player scoring (which for NWPAS is reasonably well balanced with 4-player scoring), and player is DQ'd from rest of tourney. Thus if the player does qualify, they get lowest qualifying spot.
This same approach applies to anyone who needs to leave early. Happened at VFO last year, someone made it to final 4, but then had to leave before start of finals, so they got 4th place in finals.
So while using an alternate might make sense when getting started, there's also the possibility of a player having to leave mid-playoffs, what do you do then? Whatever you do then, why not just apply that same rule for a no show in the first round?