Ahh, I keep getting the title of the new 3DS game mixed up, it's echoes, my bad my bad.
On the matter with that piece though, in music there's something called motifs or leitmotifs. It is indeed the Main theme of Fire Emblem with slight variation to it. A game that makes use of motifs and leitmotifs real well is Bravely Default where you hear similar tunes replayed with variation in instrumentation as well as arrangement of the melody, etc.
But yeah, gonna stick with what I learned in music and stick with the fact it's the main them, just re-arranged.