You may want to send each program in a multi to a separate mixer channel for convenience in mixing, or for processing them with different EQs or effects. Likewise you may want to record each program on a separate track in your DAW, again for convenience and flexibility in mixing and processing. If you want to do surround mixing the Aux outs are also useful.
There are many ways to deal with these things, and if using a single stereo output works for you, that's perfectly fine. If you find that you need more flexibility for something, you have the option of using those Aux outs.