Thanks for writing such a good detailed feedback, ThrashCaptain!
The more I think about your idea of making boss fights work like checkpoints the more I like it, token count willing I'll try implementing that in the near future. My thought initially was that restarting at the very beginning was a natural time punishment for dying, but getting a checkpoint as a reward for destroying a boss sound like a good reward for the time invested on it.
As for your the other case, I noticed the flaw when I was developing it, but thought it wouldn't be as prominent as this only happens in one room. I'll try fixing that as well somehow.
Thanks again and definitely check out my other games here on itch.io, would be great to hear what you think about those too. :)