I've noticed the screen shots of this mod and SS 6.4 having not played either...or at least not SS for years, showing the standard super high banners, that look well so crap to be frank. Im sure when i played MTW2 i either played with lovely crafted flags or very short banners!!
Flags became used by the military in the period in question and following some of the great flag mods for ETW / NTW im amazed no-ones seems to have incorporated any into this mod or indeed SS!, at least we could have small 'flag size' banners.
I've never had an issue with identifying units in battle and indeed, the chaos that would ensure SHOULD prove difficult to ID in reality, but most of all, they would just look right as the the original totem poles look wrong!