I don't think injuries affected this year's team as much as prior years. Judge/Stanton/Cole were mostly healthy all year. We did have a lot of supporting players miss time but I think the underperformance of healthy players was the biggest issue (primarily DJ, Torres, Frazier, Gio).
And Pyth record is a pointless stat so I don't think it proves anything. A team can win a single game by 20 runs and then lose the next 20 by 1 run, and Pyth record would suggest that they should be .500. The Yankees have had a highly ranked bullpen over the last decade and have won more close games because of it, so it would make sense for their expected Win% to be lower.