Also, if you reduce the number of players per row, then the players will be larger too. The more players it has to put in each row, the more it has to scale them down to fit into the row. So instead of 5 rows, maybe try 6 or 7 rows with less players per row. That will make them larger and also wil take up more vertical space too with more rows. Combine that with the player scaling and you should make it it fine.
Also, be sure to check out the setting on perspective scaling too.
Last thin, I really recommend shooting full body for team build, not cropping. It will match the players true height better if there are feet. Without feet, yo may want to change the face/feet alignment to 0 and have it align the faces. This will cause the bottom of the cutouts to not align because if the faces are aligned, the bottom can’t be. However, I’m assuming that you are going to cover the bottom with graphics anyway.
Look at the crops…. I’m assuming you may have cropped in post before running through EZ Team Builder. If so then that may be why the scaling is different between images.