You're definitely not overthinking it! The chords are... funky to say the least. I try to do that sometimes, to make overcomplicated (yet hopefully nice-sounding) chord progressions. So the surprise is expected!
I am also very glad you like the "polyrhythmic" part (as someone else called it). I wasn't sure what people would think of it. For a boss-fight it felt not too out-of-place, as boss-fights often try to make people feel uneasy or caught-off-guard. I really love that you imagine the fight being a pain in the ass! xD
"You really crossed a gap in terms of composition with the NitroJam". Thanks man!! :'D