### Godot version

4.0 beta 15

### System information

Windows 10

### Issue description

When ticking `apply_root_scale` the scale is not applied to custom collision shape set in importer.
This apply for `shape_type`  Box, Sphere, Cylinder and Capsule

_I tried to fix it myself but i'm a bit confused on how to have acces to the `apply_root_scale` and `root_scale` at the moment where the shape is generated_

### Steps to reproduce

- Add a 3d model.
- Generate physics for the mesh
- Select a `shape_type` for example Box
- Add `root_scale` != 1 and tick `apply_root_scale`

### Minimal reproduction project

[BoxColliderImport.zip](https://github.com/godotengine/godot/files/10500751/BoxColliderImport.zip)

rot_x = &md.cam_rot_x;
		rot_y = &md.cam_rot_y;
		zoom = &md.cam_zoom;
	}
	Ref<InputEventMouseMotion> mm = p_input;
	if (mm.is_valid() && (mm->get_button_mask().has_flag(MouseButtonMask::LEFT))) {
		(*rot_x) -= mm->get_relative().y * 0.01 * EDSCALE;
		(*rot_y) -= mm->get_relative().x * 0.01 * EDSCALE;
		(*rot_x) = CLAMP((*rot_x), -Math_PI / 2, Math_PI / 2);
		_update_camera();
	}
	Ref<InputEventMouseButton> mb = p_input;
	if (mb.is_valid() && mb->get_button_index() == MouseButton::WHEEL_DOWN) {
		(*zoom) *= 1.1;
		if ((*zoom) > 10.0) {
			(*zoom) = 10.0;
		}
		_update_camera();
	}
	if (mb.is_valid() && mb->get_button_index() == MouseButton::WHEEL_UP) {
		(*zoom) /= 1.1;
		if ((*zoom) < 0.1) {
			(*zoom) = 0.1;
		}
		_update_camera();
	}
}
void SceneImportSettings::_re_import() {
	HashMap<StringName, Variant> main_settings;
	main_settings = defaults;