### 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)

r_options->push_back(ImportOption(PropertyInfo(Variant::FLOAT, "nodes/root_scale", PROPERTY_HINT_RANGE, "0.001,1000,0.001"), 1.0));
	r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "meshes/ensure_tangents"), true));
	r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "meshes/generate_lods"), true));
	r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "meshes/create_shadow_meshes"), true));
	r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "meshes/light_baking", PROPERTY_HINT_ENUM, "Disabled,Static (VoxelGI/SDFGI),Static Lightmaps (VoxelGI/SDFGI/LightmapGI),Dynamic (VoxelGI only)", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), 1));
	r_options->push_back(ImportOption(PropertyInfo(Variant::FLOAT, "meshes/lightmap_texel_size", PROPERTY_HINT_RANGE, "0.001,100,0.001"), 0.2));
	r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "skins/use_named_skins"), true));
	r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "animation/import"), true));
	r_options->push_back(ImportOption(PropertyInfo(Variant::FLOAT, "animation/fps", PROPERTY_HINT_RANGE, "1,120,1"), 30));
	r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "animation/trimming"), false));
	r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "animation/remove_immutable_tracks"), true));
	r_options->push_back(ImportOption(PropertyInfo(Variant::STRING, "import_script/path", PROPERTY_HINT_FILE, script_ext_hint), ""));
	r_options->push_back(ImportOption(PropertyInfo(Variant::DICTIONARY, "_subresources", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR), Dictionary()));
	for (int i = 0; i < post_importer_plugins.size(); i++) {
		post_importer_plugins.write[i]->get_import_options(p_path, r_options);
	}
	for (Ref<EditorSceneFormatImporter> importer_elem : importers) {
		importer_elem->get_import_options(p_path, r_options);
	}
}
void ResourceImporterScene::_replace_owner(Node *p_node, Node *p_scene, Node *p_new_owner) {
	if (p_node != p_new_owner && p_node->get_owner() == p_scene) {
		p_node->set_owner(p_new_owner);
	}
	for (int i = 0; i < p_node->get_child_count(); i++) {
		Node *n = p_node->get_child(i);
		_replace_owner(n, p_scene, p_new_owner);
	}
}
Array ResourceImporterScene::_get_skinned_pose_transforms(ImporterMeshInstance3D *p_src_mesh_node) {