Disabling warnings for GDScript does not work

[Chaosus]

Godot version

dbd1524

System information

Windows 11

Issue description

Warnings appearing regardless of the state of that flag:

Steps to reproduce

• Create a new project with default scene
• Attach a default script:

extends Node3D


# Called when the node enters the scene tree for the first time.
func _ready():
	pass # Replace with function body.


# Called every frame. 'delta' is the elapsed time since the previous frame.
func _process(delta):
	pass

• Try to disable that option and run the debugging.

Minimal reproduction project

Too easy to reproduce even with default script

[Calinou]

Related to #56592.