A part of the problem is that you are mistaken. See the Playoff Format found at the bottom of this page
During the stage playoffs, yes, it doesn't matter what division you are in, it's the top 4 teams for the stage. But during the Post Season Playoffs (the real finals) your division absolutely matters.
Six teams participate in the Postseason Playoffs. The top finisher (based on match record) from each Division earns a first-round bye. The remaining four slots are filled by the four Teams with the best match win/loss records during the entire Regular Season (not including the Preseason Tournament or Stage Playoffs).
So for the Postseason Playoffs, you have the top team from each division in (even if the top team might be in 8th place overall, for example). The other four slots are filled with the four teams with the highest records (excluding the two top teams from each division), regardless of division.
So yeah, division does absolutely matter once the Postseason rolls around. Until then, there is no effect though (except perhaps for alternating which team is considered the home team and which is the away team (which only alters the skins used in the game - team color or white).
Additionally, a team plays 20 matches against each division for a total of 40 per season.
A full quadruple ronud robin with 12 teams would be 44 matches, so while a team plays against all teams in their division four times, they only play three times against four of the six teams in the other division.