I expect the first deluxe box will be Shadowlands, and given the human-centric focus of the story in this version of the game I would expect to see something like the early Spider Clan pre-Iweko's Idiot Bargain for the Shadowlands. At least in part. If we get multiple strongholds over time, I would think that there would end up being a Lost stronghold and a Horde stronghold in there, with the former focusing more on mechanics to represent infiltrating Rokugani society, and the Horde being big dumb monsters.
As long as it is not this games equivalent of -19 honor and cannot lose by dishonor I do not think the Shadowlands will be a problem mechanically.