Create a new scoring title stat (because there aren't enough already). It'll only be applied to two players and determine which one wins the scoring title. Take the player (A) who has the most points and divide those points by the PPG of the player (B) with the highest PPG. Then for player B, take their total points and divide it by the PPG of player A.
That way if someone has an absurd PPG, but misses the total by a few points due to injury, they can win, but having a slightly better PPG and an injury or load management won't win out over someone who got higher counting stats by playing all season.
Using this method, to beat a hypothetical player scoring 30 ppg and playing every game (2460 pts), a scoring champ with 31 ppg would need to play 77 games to win (2387 pts), 32 ppg would need 73 games (2336 pts), and 33 ppg would require only 68 games (2244 pts).
Looking at the finer margins, I think this method favors high PPG, so maybe tipping the scales a bit by squaring the point totals or dividing by both ppg and points totals for the other player (or both methods) to make total points a bit more valued. For example squaring both player's point totals and dividing by their opponent's point total as ppg makes that hypothetical 33 ppg player play 73 games and score 2409 points (with 73 games, 32.75 ppg and 2390 points would beat our 30ppg ironman).
Growing up, I remember watching soccer tournaments with structures like this in that the top team in every group advances, but then some, but not all second place teams go through based on goal differential or something.
Those teams were called "lucky losers", not wildcards. When you look at it like that, every team blew their shot when they didn't win the group, only a couple lucky ones got given a second chance on tiebreakers. So yeah, it's unfair, but someone has to get lucky for it to work out.
I think the tournament structure is flawed for other reasons, but it's basically a single elimination tournament with a few dice rolls that let you survive a loss in the group stage. It just adds an element of luck to the single elimination format (which already has a huge element of luck), so I don't see that as a major issue.