I replayed it too to get the benefit. The first time I played the boss I only had one heart with each respawn, the second time I had four hearts. Was there something in-game that determines that or was it a bug the first time
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1 heart meant it was the hardest difficulty (so you did a lot of time jump), 4 is the 2nd easiest
Higher difficulty give you less health and make the boss attack faster
When you reach the boss he tells you how many teleportations you did and the line he said right before you fight him change depending of the difficulty too
So yeah, definitely intended behavior!
Ah ok, when he said it would be more difficult, I assumed it was solely because the added number of attacks. It definitely scales up the difficulty to have more attacks, quicker, and less health! In an expanded game, it could be neat to have different elements be tied to the various boss elements. For example, the number of time switches determines how many times the boss attacks while using items more (like freezes enemies a ton of times) will make the attacks faster and so on and so forth.
Again, neat concept!