Then you aren't doing something correctly. Because it does work. Either you are missing a step, or are adding a step, or aren't setting the profiles for your team, one profile for all the other teams.
I have TWO profiles that I made. One is TIGERS that I use for the Detroit Tigers. The other is "OTHER TEAMS" that I set for the other 29 teams.
For the "TIGERS" profile I have everything set to manual, except scouting.
For "OTHER TEAMS" I have everything on AUTO, except Lineups/Rotations, Injury Management, and Free Agency.
I have "TIGERS" assigned to the Tigers, and "OTHER TEAMS" assigned to the other 29 teams.
It works perfectly.
Here is a video showing that the options do stick for each profile.

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