### 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)

colshape->set_shape(sphereShape);
			}
			sb->add_child(colshape, true);
			colshape->set_owner(sb->get_owner());
		}
	} else if (_teststr(name, "rigid") && Object::cast_to<ImporterMeshInstance3D>(p_node)) {
		if (isroot) {
			return p_node;
		}
		ImporterMeshInstance3D *mi = Object::cast_to<ImporterMeshInstance3D>(p_node);
		Ref<ImporterMesh> mesh = mi->get_mesh();
		if (mesh.is_valid()) {
			Vector<Ref<Shape3D>> shapes;
			if (r_collision_map.has(mesh)) {
				shapes = r_collision_map[mesh];
			} else {
				_pre_gen_shape_list(mesh, shapes, true);
			}
			RigidBody3D *rigid_body = memnew(RigidBody3D);
			rigid_body->set_name(_fixstr(name, "rigid_body"));
			p_node->replace_by(rigid_body);
			rigid_body->set_transform(mi->get_transform());
			p_node = rigid_body;
			mi->set_transform(Transform3D());
			rigid_body->add_child(mi, true);
			mi->set_owner(rigid_body->get_owner());
			_add_shapes(rigid_body, shapes);
		}
	} else if ((_teststr(name, "col") || (_teststr(name, "convcol"))) && Object::cast_to<ImporterMeshInstance3D>(p_node)) {
		ImporterMeshInstance3D *mi = Object::cast_to<ImporterMeshInstance3D>(p_node);