### 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)

Ref<Texture2D> icon = get_theme_icon(SNAME("Mesh"), SNAME("EditorIcons"));
	TreeItem *item = p_tree->create_item(p_parent);
	item->set_text(0, p_mesh->get_name());
	item->set_icon(0, icon);
	bool created = false;
	if (!mesh_set.has(p_mesh)) {
		mesh_set.insert(p_mesh);
		created = true;
	}
	item->set_meta("type", "Mesh");
	item->set_meta("import_id", import_id);
	item->set_tooltip_text(0, vformat(TTR("Import ID: %s"), import_id));
	item->set_selectable(0, true);
	if (p_tree == scene_tree) {
		mesh_data.scene_node = item;
	} else {
		mesh_data.mesh_node = item;
	}
	item->set_collapsed(true);
	for (int i = 0; i < p_mesh->get_surface_count(); i++) {
		Ref<Material> mat = p_mesh->surface_get_material(i);
		if (mat.is_valid()) {
			_fill_material(p_tree, mat, item);
		}
	}
	if (created) {
		_fill_mesh(mesh_tree, p_mesh, mesh_tree->get_root());
	}
}
void SceneImportSettings::_fill_animation(Tree *p_tree, const Ref<Animation> &p_anim, const String &p_name, TreeItem *p_parent) {