### 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)

state.canvas_instance_batches[state.current_batch_index].shader_variant = CanvasShaderGLES3::MODE_INSTANCED;
					state.instance_data_array[r_index].flags |= FLAGS_INSTANCING_HAS_COLORS;
					state.instance_data_array[r_index].flags |= FLAGS_INSTANCING_HAS_CUSTOM_DATA;
					if (particles_storage->particles_has_collision(particles) && texture_storage->render_target_is_sdf_enabled(p_render_target)) {
						
						Transform2D xform = p_item->final_transform;
						GLuint sdf_texture = texture_storage->render_target_get_sdf_texture(p_render_target);
						Rect2 to_screen;
						{
							Rect2 sdf_rect = texture_storage->render_target_get_sdf_rect(p_render_target);
							to_screen.size = Vector2(1.0 / sdf_rect.size.width, 1.0 / sdf_rect.size.height);
							to_screen.position = -sdf_rect.position * to_screen.size;
						}
						particles_storage->particles_set_canvas_sdf_collision(pt->particles, true, xform, to_screen, sdf_texture);
					} else {
						particles_storage->particles_set_canvas_sdf_collision(pt->particles, false, Transform2D(), Rect2(), 0);
					}
					r_sdf_used |= particles_storage->particles_has_collision(particles);
				}
				state.canvas_instance_batches[state.current_batch_index].command = c;
				state.canvas_instance_batches[state.current_batch_index].command_type = c->type;
				_prepare_canvas_texture(state.canvas_instance_batches[state.current_batch_index].tex, state.canvas_instance_batches[state.current_batch_index].filter, state.canvas_instance_batches[state.current_batch_index].repeat, r_index, texpixel_size);
				state.instance_data_array[r_index].modulation[0] = base_color.r * modulate.r;
				state.instance_data_array[r_index].modulation[1] = base_color.g * modulate.g;
				state.instance_data_array[r_index].modulation[2] = base_color.b * modulate.b;
				state.instance_data_array[r_index].modulation[3] = base_color.a * modulate.a;
				for (int j = 0; j < 4; j++) {
					state.instance_data_array[r_index].src_rect[j] = 0;
					state.instance_data_array[r_index].dst_rect[j] = 0;
					state.instance_data_array[r_index].ninepatch_margins[j] = 0;