K
I'm not entirely sure what you're referring to here, as the only enemy that changes their level during combat is the first fight against Adam, where leveling up is his primary mechanic, and he learns moves and abilities as the fight progresses.
From my experience (over 100 hours of gameplay), there is no level adjustment at all with machine lifeforms. The only enemies whose levels scale with yours are the wild moose and boars, which is why they become the only real threat when you've maxed out your level. Regular enemies and bosses have set levels at different points in the game. This is especially apparent when you unlock Chapter Select and go to previous chapters (or even previous routes) and go through the areas again.
For instance, I went back to fight Beauvoir again (the amusement park boss you mentioned), my AI-controlled 9S killed her in a single hit and kept her down for several minutes, until I realized she needed to be up long enough to go back onto the stage to move the fight to the next stage, at which point, I had to turn his AI to passive.
If I remember correctly, enemies will never be higher than level 60-65, aside from the golden bunny statue and DLC arenas, where enemies have set levels that exceed 100 in some cases. Additionally, bosses (aside from the one case I mentioned) will never change levels.
I don't think difficulty level has anything to do with enemy level, either. I believe it just makes enemies more powerful without adjusting their level.