This sounds like you are trying to overcomplicate something...If the phase issues are caused by reflections that you do not have control over, then just do the following:
Tune to your curve, then measure the speakers in pairs. If you need to adjust levels, do so in pairs. If your midbass are 3db higher than your mids/tweets, adjust both mids/tweets equally +3db (to keep their side to side level the same difference). Similar if you adjust your midbass. If it is tuned flat, it is tuned flat...it doesn't really matter what target level.
Plenty of people don't even care about target level and just tune each speaker the best, then adjust levels to match after they tune. That order doesn't really matter.