Yeah but you need to do this in order to keep the positions fair. You want to have the strongest and weakest player of both teams to be in the same position to their (rotational) mirror. The asymmetry it creates is often beneficial for the gameplay anyways. But moreover, you need this to keep it fair. Imagine the case were on one team the strongest player gets a spot with 8 mexes and on the other team the strongest player gets 25 mexes. That's way worse.
I checked out the 3v3 replay you've posted. There is nothing wrong there in terms of the positions. Sure the weaker player has to fight the stronger one, but I don't think that is necessarily bad there. At least the strongest players start in the same relative positions, which is more important.