The way I understood it, George Lucas wanted the clones of Episode III to have graphitti on their armour, as a nod to the American soldiers in Viet Nam. (Can't remember where I read that.)
This concept was taken and further developed to have the markings denote the units, rather than individual trooper preference.
This makes a lot of sense; Esprit de Corps is an important part of military units. That's why so much thought can go into unit insignia patches and flags in the real world. Often every little piece of the badge has a special meaning. Each color is chosen for something, or is given a meaning after the fact.
My old unit's brigade patch was a wolf howling at the moon. The wolf was adopted because it's an intelligent and capable predator, but it is best when working with others of its kind. So each of the Regiments in the brigade were formidable, but together the Regiments of the Brigade were even more capable.
And of course, each Regiment that made up the brigade had its own insignia, my Regiment's cap badge was a stag's head, over a maltese cross, in a wreath of maple leaves, with the Queen's crown above and the Canadian beaver beneath, with the latin motto 'Paratus'.
I can see clones being very proud of their legion markings, and knowing the 'why' of every colour and every mark, and what it means to wear it....and being potentially angry to see anyone wear it who wasn't entitled.
