The portions are based on creating optimal health. For those needing to gain weight, it's important to make sure they eat all the recommended portions of every food group. For those looking to lose weight it's important to not go over the recommended portions. For general health maintenance, the portions tell you the ratio of meat to veggie to grain etc.
Whether you need to lose,gain, or maintain, you want to eat the right proportions of foods. Many people eat far fewer veggies, and far more proteins and grains, than they should. The SWAMI portion recommendations guide people to changing those ratios. If you completely ignore this aspect of SWAMI, you won't obtain the maximum health benefits that SWAMI can provide.
SWAMI is a complex computer program, but the human body is even more complex. Sometimes the portions need to be tweaked. I know I felt faint and weak when I strictly followed SWAMI portion recommendations for 2 days in a row- so I increased my fat and protein portions, while continuing to follow the restrictions on grains and fruits. Others have found that they can't eat all that SWAMI recommends so they eat less.