If over 1,000 people didn't have a problem identifying different factions maybe it isn't an issue.
It's just that if I'm introducing the game I'll probably select 4 factions beforehand (for the first game or two with new players). If the players weren't involved in the drafting stage and are just learning the game I can see lots of "who controlling those/ that" type questions.
And I'll admit my obsessive compulsive side wants to see each team identified.
I think you underline an important thing: as players draft the miniatures at the beginning of the game and as all miniatures are unique (except from troops but they remain together), I think it is quite easy to know who belongs to whom…