### 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)

icon = get_theme_icon(SNAME("PackedScene"), SNAME("EditorIcons"));
		item->set_text(0, "Scene");
	}
	item->set_icon(0, icon);
	item->set_meta("type", "Node");
	item->set_meta("class", type);
	item->set_meta("import_id", import_id);
	item->set_tooltip_text(0, vformat(TTR("Type: %s\nImport ID: %s"), type, import_id));
	item->set_selectable(0, true);
	if (!node_map.has(import_id)) {
		NodeData nd;
		if (p_node != scene) {
			ResourceImporterScene::InternalImportCategory category;
			if (src_mesh_node) {
				category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MESH_3D_NODE;
			} else if (Object::cast_to<AnimationPlayer>(p_node)) {
				category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_ANIMATION_NODE;
			} else if (Object::cast_to<Skeleton3D>(p_node)) {
				category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_SKELETON_3D_NODE;
			} else {
				category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_NODE;
			}
			_load_default_subresource_settings(nd.settings, "nodes", import_id, category);
		}
		node_map[import_id] = nd;
	}
	NodeData &node_data = node_map[import_id];
	node_data.node = p_node;
	node_data.scene_node = item;
	AnimationPlayer *anim_node = Object::cast_to<AnimationPlayer>(p_node);