Sweeps also include reflections, but you can use various techniques to get rid of them. However, my thinking is that whatever reaches your ears should be room corrected, and that includes reflections. To get rid of reflections, you need to treat your room with acoustic treatment (Auralex etc), but whatever reflections you have should be included.
An interesting thing about reflection: if you have a specific listening position, its better to have speakers with a narrow sound dispersion, since they focus the sound more towards your ear and will result in less reflections (usually the reasoning is that wide dispersion for speakers is good).
Phase matters less than most thinks in normal room correction, I used a trial of Dirac and compared and could not hear any difference between my own REW room correction. I also talked to the developer or software rePhase and he said that room correction should be minimum-phase EQ correction and nothing else.