### 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)

}
	String global_defines;
	global_defines += "#define MAX_GLOBAL_SHADER_UNIFORMS 256\n"; 
	global_defines += "#define MAX_LIGHTS " + itos(data.max_lights_per_render) + "\n";
	GLES3::MaterialStorage::get_singleton()->shaders.canvas_shader.initialize(global_defines, 1);
	data.canvas_shader_default_version = GLES3::MaterialStorage::get_singleton()->shaders.canvas_shader.version_create();
	shadow_render.shader.initialize();
	shadow_render.shader_version = shadow_render.shader.version_create();
	{
		default_canvas_group_shader = material_storage->shader_allocate();
		material_storage->shader_initialize(default_canvas_group_shader);
		material_storage->shader_set_code(default_canvas_group_shader, R"(
// Default CanvasGroup 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);
	if (c.a > 0.0001) {
		c.rgb /= c.a;
	}
	COLOR *= c;
}
)");
		default_canvas_group_material = material_storage->material_allocate();
		material_storage->material_initialize(default_canvas_group_material);
		material_storage->material_set_shader(default_canvas_group_material, default_canvas_group_shader);
	}
	{
		default_clip_children_shader = material_storage->shader_allocate();