I think if one studies the "Manager Profiles" page of a typical league, one can see that team setting do in fact make a big difference. For example, here's a typical manager page in a 100M DH league.
http://onlinegames.strat-o-matic.com/league/stats/managers/regularseason/166029Notably, one team (my COU) allowed only 7 IBB. From there, one finds a gradual curve up to the maxium allowed, 54 IBB. One team made only 4 Sac attempts. Another made 67. There's a lot of variation in between. All of these no doubt indicate team strategy and card settings. There are also very large variations in total steal attempts (as few as 22 and as many as 500), and hit and run attempts (as few as zero—4 teams—and as many as 127). So, team and player settings are obviously having major impacts on these kinds of plays, and how often they happen.
Also, look at the closer usage on the Pitching stats page.
http://onlinegames.strat-o-matic.com/league/stats/players/pitching/166029/closers/s/0Dennis Lamp led the league in saves, while pitching just 52.1 IP. Obviously he was given the "Maximize" closer setting. On the other hand, Dale Murray pitched 318 innings as an RP. These results were clearly a product of team and card settings.
So, while a manager won't always get the exact result he wants in given game, it seems to me clear that team and player settings do have a significant impact on what happens over a season.