Hmm, the part where the boss keeps the upgrades is intentional for the game to be difficult, but it should move into the next boss when you get to the right difficulty... Not sure what you were able to do to make it so that all 3 options are the same though, but yeah, at least part of what you're saying is intentional.
Unfortunately, the programmer isn't awake at this time I don't think, I would be able to fix it if I had access to the game files (I am a programmer, just not the designated one for this project). Glad you were able to vibe with at least some parts of the game!