Doomtrain and Phantom Train are basically the same entity, but, depending on who you ask, it's either a reference to FFVI or FFVIII.

The Phantom Train in FFVI carried the dead to the afterlife. The implications of something like this being in FFXIV would be amazing, and it could possibly let us see a dear departed friend one last time.

The Doomtrain in FFVIII was a summon, who's actual name was Glasya Lobalas, that you could call on to help you fight. As there is already a Glasya Lobalas in FFXIV, I'm guessing that this is not the inspiration they are going to use for the Clockwork Doomtrain.

Also, considering that Heavensward has basically been screaming "I'M MAKING FFVI REFERENCES" since the story began, I'm guessing they're going to keep making FFVI references.