The roster in Madden has always represented a snapshot of the league as it exists right now. The results of the 2018 season generally speaking have the greatest weight in determining player ratings.
If and when Rodgers returns to his usual excellence during the 2019 season, the weekly roster updates will reflect that as Tiburon updates the snapshot of the league. Rodgers absolutely was
not his usual self last season. Whatever the reasons were to put context behind that decline - be it injuries, young receivers, scheme, his own issues; there was no one thing which was solely responsible - the resulting decreased performance level on the field still happened and Madden 20's launch ratings are accounting for that.
As to Mahomes, he literally threw 50 touchdowns last year (Aaron Rodgers has never exceeded 45 touchdown passes in a season). Mahomes was also 2nd in passer rating and 1st in Total QBR. He more earned his high ratings, lol.