And, to address a couple other points in your post:
Minor leagues: They have League Totals, too. Older versions of
OOTP used the major league League Totals everywhere, newer versions allow you to change them at every level.
Timing of Changes: I assume historical League Totals are updated each January 1, but I really don't know. Above, Spritz showed that you can change league totals any time, but really the better solution sould seem to be to change them once in a way that would make the process work based on the actual players in the league.