How will Meiji Ishin work?

You posed a good question so I did some digging on message boards back when the event had just come out and people were discussing the faction thing. I may be wrong, but I believe it is a "live" calculator similar to Solomon and some raid health bar events where-in everyone on the server works towards one faction or another. Even if that's not the case, the point of the event is to apparently progress both, hence why the ascension mats and np mats are split between the two. However, only one faction can "win."

Edit to this: You don't actually choose and lock in your faction despite what the guide suggests. You basically have marked quests for each and you fight on the side you want to get points for. It doesn't matter who you pick first or whatever you can just keep switching back and forth getting points in both and you will need to do so. However, there seems to be some kind of bonus point gain to the faction that is winning which makes it easier to clear out that faction's rewards I guess. Based on JP, it looks like Nobunaga faction was the favorite since she has some rarer mats people want. That may change for NA.