I'm yet unable to clear the 3rd boss, but I think I'll keep trying. It's a fun game, one of my favorites this jam, and it wouldn't be as dear to me if it wasn't this challenging.
The slowdown generally makes the 3rd loop more playable. In particular, I think the middle room in the 2nd set of rooms during loop 3 would have been very difficult without it. (It's still a bit volatile, but the player can simply dip in and out of the room until they get a good pattern.)
However, the slowdown during the 3rd boss is excessive enough to interfere with my enjoyment. Especially during the 3rd spell, the game runs so slowly that it is hard for me to judge how early I have to move to have time to move out of the way of the bullets. I have never cleared that spell, but it's partly due to me losing too many lives on the 2nd boss to get into the final boss with enough lives: on a good run, it should definitely be doable, so I don't think the game should be made easier. It'd just be nice if the difficulty wasn't in part due to the slowdown. (Obviously, large parts of the game would have to be rebalanced if it ran at full speed, so you may be stuck in a local minimum here.)
Also, it would be good if the game killed you after the time bonus reaches zero. The way I understand it, the scoring system is meant to reward you for being fast, since the score you lose every time unit generally is greater than what you could gain from just killing enemies. However, since the score loss due to being slow is capped, you could theoretically ignore it and farm enemies indefinitely for infinite score (and lives?).
I've talked a lot about what I don't like, but it's because the game is so good that I can list its flaws in just a short comment. Please keep up the good work!