I would prefer the Doomtown approach. Everything in the previous edition still happened, there was simply a time jump that took place, which gave time for the new factions to be introduced and for the town to start rebuilding.
Poor use of the 20 years worth of storyline they just paid for.
Because, ultimately, that's the heart of the Rokugan setting. Not the RPG splat book, not the general idea of a world split into clans. The twenty years of story that fleshed out those clans and gave them their iconic characters and moments.
L5R has had time jumps before, most recently between Celestial and Emperor. AEG were already planning for one to happen some time during Onyx.