The unclarity of the eye boss is more an artifact of it being a late addition to the game than you missing anything. It could use more feedback in general, and another pass to tune the difficulty.
The escape sequence not having it’s own music was more an artifact of not having enough time between the conception and implementation for the musician to have time to pull something together.
Spikes having more feedback, better checkpointing, and/or switching out red spikes for lava or acid would definitely help.
As far as bomb ammo goes, I think I’d make it something that spawns from enemies in the future (as well as health that is separate from vials) and/or make the damage output from bombs closer to the pipe (and make most enemies less tanky to match).
The thing I wanted to avoid was players only using bombs, though, as you pointed out, there’s enough ammo about that they can almost get there.
I like keeping melee at least a bit relevant, though how the pipe interacts with enemies needs work (especially having knockback).
Thanks for giving the game a close look!