This might be interesting, but I don't know how feasible it is given the backend of FFXIV's systems.

The train would have to move very slowly to allow players to jump on and off like you envision. Also, there's a lot of processing power in making that many destructible enemies like a train track. I'm also really concerned whether it's possible to track hp and save it between entire zones when creating a FATE (it's possible to make it, but I don't know if the current coding supports something like that. If not, it's going to cost a lot of money and time to go through it and recode it). Not to mention the server load and lag spikes when a ton of players suddenly vomit in to one zone at the same time.

Anyway, those are just my initial thoughts on it. Otherwise, I would like a more dungeon-like or larger arena for a primal fight. The Doom Train seems like it would be a good way for that to work. I'm just not certain about an open-world boss with all the gimmicks you could throw at the players.