It's a alot harder than the other one I came up with, but this saves a good amount of time in the any% w/o major glitches category.

by going inside the boss, while shooting and going as far as possible left while still being able to shoot him, He'll jump to the left where you can then carefully jump over his shot and kill him. It sounds complicated but its really not, so I have this video to demonstrate

I think its because when you were lagging while entering the cave you went further in than was intended which got rid of the cutscene where you walk up to the boss, which after said cutscene, the doors close. But you were moving around normally, which meant the cutscene was gone.