In my view the SE troopers are actually wearing phase 5 armour and are from the special detachment that were sent down from the star destroyer, and they had to get dirtied up real quick to fit in with the local boys.
They also have the new r & d, un-field tested, back-packs instead of the cobbled together on the job packs that the Mos Eisley troopers have put together to help them on sunny Tatooine.
And in case you are wondering, Phase 1 & 2 are epii and epiii respectively, phase 3 is the original TD armour (which hasn't been updated for those posted on the back-water planets), phase 4 armour is the last model stormtrooper armour as worn by the majority of troops (such as those on the death star) and phase 5 armour is the newer armour that is slowly rotated into use between epiv and vi, (hence some of the mis-matched armour as seen in epV). So the SE troopers are privaledged in that they get the new armour first as they are based on Vaders star destroyer?
All of the above is pure speculation.