I'm not sure how to explain the sound... But it happens when you respawn and goes back to normal after so I think it might be because of the repositioning of player character. Hard to say how the audio is set up in the tutorial as I have not watched it.
Yep, you are spot on about the colliders. Perhaps just changing the spike collision shape would have a noticeable impact.
You say you were not playtesting in Godot 4 but... You did playtest it right?