Instead of giving strokes, what if the higher seeds got mulligans?
Seeds 9-12 get two strokes (total for both rounds). That is only one stroke per round to overcome for the 32nd seeded player to get to the finals, where scores totally reset, and everyone starts on equal footing.
I actually like the format. You want most of the top names in the final, but this does give several others a decent chance to get there as well over two rounds if they are playing well. And if you play poorly, then you are certainly not guaranteed a spot in the finals.
Players also have to be incentivized throughout the year to want to do well in the points standings, since other than strokes or byes in this final tourney, they really get nothing. Maybe they should also get cash if they finish in the top 3, or 5, or whatever.