### 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)

col->set_transform(get_collision_shapes_transform(node_settings));
								base = col;
							} break;
							case MESH_PHYSICS_RIGID_BODY_AND_MESH: {
								RigidBody3D *rigid_body = memnew(RigidBody3D);
								rigid_body->set_name(p_node->get_name());
								p_node->replace_by(rigid_body);
								rigid_body->set_transform(mi->get_transform() * get_collision_shapes_transform(node_settings));
								p_node = rigid_body;
								mi->set_transform(Transform3D());
								rigid_body->add_child(mi, true);
								mi->set_owner(rigid_body->get_owner());
								base = rigid_body;
							} break;
							case MESH_PHYSICS_STATIC_COLLIDER_ONLY: {
								StaticBody3D *col = memnew(StaticBody3D);
								col->set_transform(mi->get_transform() * get_collision_shapes_transform(node_settings));
								col->set_name(p_node->get_name());
								p_node->replace_by(col);
								memdelete(p_node);
								p_node = col;
								base = col;
							} break;
							case MESH_PHYSICS_AREA_ONLY: {
								Area3D *area = memnew(Area3D);
								area->set_transform(mi->get_transform() * get_collision_shapes_transform(node_settings));
								area->set_name(p_node->get_name());
								p_node->replace_by(area);
								memdelete(p_node);
								p_node = area;