### 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)

return shapes;
	} else if (generate_shape_type == SHAPE_TYPE_CYLINDER) {
		Ref<CylinderShape3D> cylinder;
		cylinder.instantiate();
		if (p_options.has(SNAME("primitive/height"))) {
			cylinder->set_height(p_options[SNAME("primitive/height")]);
		}
		if (p_options.has(SNAME("primitive/radius"))) {
			cylinder->set_radius(p_options[SNAME("primitive/radius")]);
		}
		Vector<Ref<Shape3D>> shapes;
		shapes.push_back(cylinder);
		return shapes;
	} else if (generate_shape_type == SHAPE_TYPE_CAPSULE) {
		Ref<CapsuleShape3D> capsule;
		capsule.instantiate();
		if (p_options.has(SNAME("primitive/height"))) {
			capsule->set_height(p_options[SNAME("primitive/height")]);
		}
		if (p_options.has(SNAME("primitive/radius"))) {
			capsule->set_radius(p_options[SNAME("primitive/radius")]);
		}
		Vector<Ref<Shape3D>> shapes;
		shapes.push_back(capsule);
		return shapes;
	}
	return Vector<Ref<Shape3D>>();
}
template <class M>
Transform3D ResourceImporterScene::get_collision_shapes_transform(const M &p_options) {