Are they 3 different games or same game? Whats the deal behind these fire emblem?
OK, let me explain.
There are two different paths through the game which differentiate after a few missions and have completely different missions (including maps), playable characters and even the focus is different. One version is more hardcore in that it does not allow for grinding and has more challenging maps, whereas the other (more popular, sadly) version is more inviting, allows for grinding and has an increased focus on social interaction between the characters in the game ("Waifu simulator"-content). Game engine, story and some characters are the same, though in one game you play on one side of the war, in the other game on the other side of the war. People who bought the Special Edition have obtained both versions and additionally a third path through the game which will now be released as a DLC for the stand alone versions.
People who have bought either version still have the option to get the other version as DLC for a reduced price of 20$, so, if Nintendo is not counting this DLC as additional sales of FE Fates, then it's probably fair to count the 400k as sales for one game, if they do count the DLC as additionally sold copies of Fire Emblem Fates, then it is very difficult to get a clear picture of how many people bought Fates.