### 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].command = c;
					state.canvas_instance_batches[state.current_batch_index].shader_variant = CanvasShaderGLES3::MODE_PRIMITIVE;
				}
				_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);
				for (uint32_t j = 0; j < MIN(3u, primitive->point_count); j++) {
					state.instance_data_array[r_index].points[j * 2 + 0] = primitive->points[j].x;
					state.instance_data_array[r_index].points[j * 2 + 1] = primitive->points[j].y;
					state.instance_data_array[r_index].uvs[j * 2 + 0] = primitive->uvs[j].x;
					state.instance_data_array[r_index].uvs[j * 2 + 1] = primitive->uvs[j].y;
					Color col = primitive->colors[j] * base_color;
					state.instance_data_array[r_index].colors[j * 2 + 0] = (uint32_t(Math::make_half_float(col.g)) << 16) | Math::make_half_float(col.r);
					state.instance_data_array[r_index].colors[j * 2 + 1] = (uint32_t(Math::make_half_float(col.a)) << 16) | Math::make_half_float(col.b);
				}
				_add_to_batch(r_index, r_batch_broken);
				if (primitive->point_count == 4) {
					
					_update_transform_2d_to_mat2x3(base_transform * draw_transform, state.instance_data_array[r_index].world);
					_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);
					for (uint32_t j = 0; j < 3; j++) {
						int offset = j == 0 ? 0 : 1;
						
						state.instance_data_array[r_index].points[j * 2 + 0] = primitive->points[j + offset].x;
						state.instance_data_array[r_index].points[j * 2 + 1] = primitive->points[j + offset].y;
						state.instance_data_array[r_index].uvs[j * 2 + 0] = primitive->uvs[j + offset].x;
						state.instance_data_array[r_index].uvs[j * 2 + 1] = primitive->uvs[j + offset].y;
						Color col = primitive->colors[j + offset] * base_color;
						state.instance_data_array[r_index].colors[j * 2 + 0] = (uint32_t(Math::make_half_float(col.g)) << 16) | Math::make_half_float(col.r);
						state.instance_data_array[r_index].colors[j * 2 + 1] = (uint32_t(Math::make_half_float(col.a)) << 16) | Math::make_half_float(col.b);
					}
					_add_to_batch(r_index, r_batch_broken);