I would suspect that palpatine on the Upsilon is a temporary thing - I believe that the First Order, Empire, Rebel, and Resistance factions will become seperate at some point. The reason they aren't now, is because there are currently two ships. One for each faction. As we get more ships to fill out these current sub-factions, they become more likely to stand on their own.
I expect a FAQ update that states they are seperate factions in a couple years time.
Why? Because there are cards out there that don't state or have any indication what time period they are from.
Is mara Jade for example from the ot? Or is she from tfa era?
Maybe you know, that answer but believe it or not there are people out there who don't.
Maybe Disney will release something and suddenly she is no longer from the era you once knew. Mara Jade is one example, what about nein numb? He's around during the tfa era, so can he be used for both? The same can be said about different upgrade and pilots. Kyle Katarn. Again maybe not everyone knows which era he's from, and again Disney could change that with a comic/show/movie/book
There is absolutely nothing stopping players from hosting their own events and play with these restrictions, but ffg probably won't bother.
Let's not forget that when they are play testing, it's being play tested as one faction. To separate it into its own faction down the road can have balancing issues