Even if you can't disable encounters entirely there's a "reduced encounter" mode that doesn't require beating the boss and in the most recent dungeon I think you can disable encounters even without defeating the boss.One thing I can't help complaining about this game is you cannot avoid encountering enemies while doing puzzles around the map. The frequent encounter is a big distraction to the puzzling and really interrupts one's thinking. It's not like I hate puzzling though. The first time I had this feeling was when I was doing the lotus leaves puzzle in the sewer and as the puzzle is becoming more complicated I feel like we really need an option to rush the boss first then back for the puzzle part with silent mode.
The encounter rate does feel a bit oppressive when you don't reduce it though.