### Godot version

4.1.1-stable

### System information

Windows 10

### Issue description

When the project loads in editor, all the settings defined in project settings will be loaded over the default values, but when running the game nearly 95% of them will be ignored resulting in just loading the default settings.

here it's just loading only 4 variables from project setting and i have added the fifth in this pull request https://github.com/godotengine/godot/pull/80151
![image](https://github.com/godotengine/godot/assets/53877170/926168a6-e6d3-4983-b59d-7fd202db681d)

material_storage->shader_initialize(default_clip_children_shader);
		material_storage->shader_set_code(default_clip_children_shader, R"(
// Default clip children shader.
shader_type canvas_item;
render_mode unshaded;
uniform sampler2D screen_texture : hint_screen_texture, repeat_disable, filter_nearest;
void fragment() {
	vec4 c = textureLod(screen_texture, SCREEN_UV, 0.0);
	COLOR.rgb = c.rgb;
}
)");
		default_clip_children_material = material_storage->material_allocate();
		material_storage->material_initialize(default_clip_children_material);
		material_storage->material_set_shader(default_clip_children_material, default_clip_children_shader);
	}
	default_canvas_texture = texture_storage->canvas_texture_allocate();
	texture_storage->canvas_texture_initialize(default_canvas_texture);
	state.time = 0.0;
}
RasterizerCanvasGLES3::~RasterizerCanvasGLES3() {
	singleton = nullptr;
	GLES3::MaterialStorage *material_storage = GLES3::MaterialStorage::get_singleton();
	material_storage->shaders.canvas_shader.version_free(data.canvas_shader_default_version);
	shadow_render.shader.version_free(shadow_render.shader_version);
	material_storage->material_free(default_canvas_group_material);
	material_storage->shader_free(default_canvas_group_shader);
	material_storage->material_free(default_clip_children_material);
	material_storage->shader_free(default_clip_children_shader);
	singleton = nullptr;
	glDeleteBuffers(1, &data.canvas_quad_vertices);