The organ for the good side and the electric guitar for the evil side. Super efficient, no need for embellishment.
On the chords, my ear hears Am but your score is in Dm. This gives the Gm so surprising. For me the dominant E is the V but you thought it in V/V which is great. I was surprised with every loop.
But that's not all! At 0'45" you have fun putting the guitar on a kind of 5/4 when the rest continues in 4/4. It's like the two parts are independent (like the two parts of the boss) and it's great! I can see the fight being a pain in the ass like Ornstein and Smough in Dark Souls.
Maybe I'm overthinking it :)
It definitely sounds like a good and evil boss fight to me!
You really crossed a gap in terms of composition with the NitroJam 👍