### 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)

if (Object::cast_to<ImporterMeshInstance3D>(p_node)) {
		ObjectID node_id = p_node->get_instance_id();
		for (int i = 0; i < post_importer_plugins.size(); i++) {
			post_importer_plugins.write[i]->internal_process(EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_MESH_3D_NODE, p_root, p_node, Ref<Resource>(), node_settings);
			if (ObjectDB::get_instance(node_id) == nullptr) { 
				break;
			}
		}
	}
	if (Object::cast_to<Skeleton3D>(p_node)) {
		ObjectID node_id = p_node->get_instance_id();
		for (int i = 0; i < post_importer_plugins.size(); i++) {
			post_importer_plugins.write[i]->internal_process(EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_SKELETON_3D_NODE, p_root, p_node, Ref<Resource>(), node_settings);
			if (ObjectDB::get_instance(node_id) == nullptr) { 
				break;
			}
		}
	}
	if (Object::cast_to<ImporterMeshInstance3D>(p_node)) {
		ImporterMeshInstance3D *mi = Object::cast_to<ImporterMeshInstance3D>(p_node);
		Ref<ImporterMesh> m = mi->get_mesh();
		if (m.is_valid()) {
			if (!r_scanned_meshes.has(m)) {
				for (int i = 0; i < m->get_surface_count(); i++) {
					Ref<Material> mat = m->get_surface_material(i);
					if (mat.is_valid()) {
						String mat_id = mat->get_meta("import_id", mat->get_name());
						if (!mat_id.is_empty() && p_material_data.has(mat_id)) {
							Dictionary matdata = p_material_data[mat_id];
							{