### 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)

for (Node3D *node_3d : p_dictionary.node_3ds) {
		if (node_3d) {
			node_3d->set_position(p_scale * node_3d->get_position());
			Skeleton3D *skeleton_3d = Object::cast_to<Skeleton3D>(node_3d);
			if (skeleton_3d) {
				for (int i = 0; i < skeleton_3d->get_bone_count(); i++) {
					Transform3D rest = skeleton_3d->get_bone_rest(i);
					skeleton_3d->set_bone_rest(i, Transform3D(rest.basis, p_scale * rest.origin));
					skeleton_3d->set_bone_pose_position(i, p_scale * rest.origin);
				}
			}
		}
	}
	for (Ref<ImporterMesh> mesh : p_dictionary.importer_meshes) {
		_rescale_importer_mesh(p_scale, mesh, false);
	}
	for (Ref<Skin> skin : p_dictionary.skins) {
		_rescale_skin(p_scale, skin);
	}
	for (Ref<Animation> animation : p_dictionary.animations) {
		_rescale_animation(p_scale, animation);
	}
}
void _populate_scalable_nodes_collection(Node *p_node, ScalableNodeCollection &p_dictionary) {