Having lot of different and unbalanced factions means there will be some with above average unit combinations, and majority of the MP population might choose to only play these elite factions. But as long as these factions are balanced compared to each other, games will be balanced as these are actually the better ones
The difference is, in a moded scenario, there's no other options besides playing the few "balanced" pre choosen elite factions. There were always people playing the seemly less effective factions and did well, important thing is leaving the room for players to excercise that option.

And one thing I've always hated about MP moding. You are spliting the community. It takes a sizable pool of MP players for the good ones to actually distinguish themselves and establish competition within the community. Why attempt to split the population to different mod pools before the game even release? What's the point of playing a war game where there's little or no competition?