It does make a difference.
I've done it for this weekend. Dropping my starting lineup from 7 stars to 3 before the draw. I now face the weakest team in the opposition association for today's semi.
Although nothing is guaranteed, supposing I win both games, the other 5 members only have to win 50% of their matches to put us in the final.
Manipulating associations like this increases the possibility of reaching the final and at least picking up the 25 bonus points for finishing 2nd.