I'd have to play with the math, but at first glance, a first-round-late-arrival loss is harder to recover from than a first-round-played-match loss (because event tardiness is the first tiebreaker). If that player really wanted to "game" the system smartly, they'd concede/throw the first round match rather than show up late.
So opp-win percentages don't even come into play for tardy players.
Now, regarding how it affects pairings, I'd hope TOM is fixed and does it correctly (based purely on records-first-random-second); otherwise, the issue here is with TOM, not the player.
So yeah Ken, I don't understand that issue -- if indeed, that's Patricia's rationale.