Yeh but the loser gets another shot at making the GF by playing the winner of the other game. Its how its done in some competitions in the world IIRC. I don't really see any other fair way of doing it with 6. You could have Finals Round 1 A 3rd 6th B 4th 5th Finals Round 2 C Win A 1st D Win B 2nd Or C Win A 2nd D Win B 1st Grand Final Win C Win D But either way 2nd place could end up playing a "weaker" team than 1st.
Well in the other way the team that comes 2nd has to beat the best side to make the final and the 3rd placed team only has to play inferior sides.
If the 2nd place team loses to the 1st place team he has another chance by playing the winner of the other quarter finalists... a team he probably would have had to play anyway. At least this method we won't have a grand final between 6th and 5th