Thank you for playing! I'll check your game out, love to see another approach to the idea.
Good eye, yeah, the stuttering is due to the pulsing. The way I have it setup, Godot compiles the shader each time the objects spawn. I fixed it for the clouds but didn't have time for the red pulses! It's mainly on the web version, didn't see an issue on desktop version on my machine.
Level 8 on the web build is impressive!