There was a very brief time on the design team when we were lead to believe that we at AEG would be resurrecting L5R as an LCG before we found out it had been sold to FFG.
One of the things we discussed was the likelihood that we would have only four factions instead of the normal amount, each faction representing one of the four "major powers" vying for control of Rokugan. Since it was a time jump after the conclusion of Onyx, it was basically a "War of three Emperors" situation.
1) The 'Rightful Emperor' Kanpeki and those loyal to him
2) An alliance basically run by Akodo Kano and Hida Toranosuke, the two champions of those Clans, with the possibility of a "Lion Heir/Son of Kaneka" angle being worked in there (probably to the chagrin of those two leaders), who were allied with the Naga, sort of the defacto "good guys" faction
3) An alliance of the Unicorn, Phoenix, and Crane operating out of the Second City, probably with Shibatsu as a figurehead, mostly masterminded by Suikihime
4) An unnamed fourth faction we were still fleshing out that might have appeared later.
So the clans were mostly divided between one or more of these factions, with most Clans having people in more than one.
I may be misremembering some of the details (we never committed any of this to documentation), but you get the jist of it.
I could very easily see them doing something like that, regardless of the era they set it in.