### 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)

mat->set_name(_fixstr(mat->get_name(), "vcol"));
				}
			}
		}
	}
	if (Object::cast_to<AnimationPlayer>(p_node)) {
		AnimationPlayer *ap = Object::cast_to<AnimationPlayer>(p_node);
		
		Node *ap_root = ap->get_node(ap->get_root());
		NodePath path_prefix = p_root->get_path_to(ap_root);
		bool nodes_were_renamed = r_node_renames.size() != 0;
		List<StringName> anims;
		ap->get_animation_list(&anims);
		for (const StringName &E : anims) {
			Ref<Animation> anim = ap->get_animation(E);
			ERR_CONTINUE(anim.is_null());
			
			for (int i = 0; i < anim->get_track_count(); i++) {
				NodePath path = anim->track_get_path(i);
				for (int j = 0; j < path.get_name_count(); j++) {
					String node = path.get_name(j);
					if (_teststr(node, "noimp")) {
						anim->remove_track(i);
						i--;
						break;
					}
				}
			}
			
			if (nodes_were_renamed) {