Well, the two versions will share a protagonist, gameplay mechanics, and world setting. Since those generally change with every Fire Emblem game, it seems difficult to assert that each version will contain a full game's worth of unique content.

Another reason to believe that they are not completely unique game is that development time was relatively short. It seems difficult to believe that they developed two completely unique games in three years. Relying on a common framework and creating variation around it is likelier.

Finally, an indicator that those are not two fully unique games is the price point. They sell the second game at a heavily discounted rate, ie. pretty much the cost of one piece of DLC. (A pricy DLC, but 15$ for a DLC is the cost of an expansion-sized DLC for many games).

Why would they sell the second game at such a big discount if the two games were completely unique?

If it was true that the two games were unique, then there would be a full price for each game. The fact that they reduce the price of the second game hints that even they do not think the second game is worth a full price.

I am not necessarily saying that this is a bad thing. It is perfectly fine to ship an experience that is less than a full priced game's worth if you sell it for less than full price.

I note in closing that this is why I find this whole debate strange. The "This business model is fine" camp is painting itself in a corner by setting the bar so high. If the second game sells for less than half the cost of the first, there is no need to argue for two full games to justify the second price point. Claiming that whatever different content there is will suffice to meet the second, lower price point would be quite sufficient to make their case.