### 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)

return animation_importer ? "animation_library" : "scene";
}
String ResourceImporterScene::get_visible_name() const {
	return animation_importer ? "Animation Library" : "Scene";
}
void ResourceImporterScene::get_recognized_extensions(List<String> *p_extensions) const {
	for (Ref<EditorSceneFormatImporter> importer_elem : importers) {
		importer_elem->get_extensions(p_extensions);
	}
}
String ResourceImporterScene::get_save_extension() const {
	return animation_importer ? "res" : "scn";
}
String ResourceImporterScene::get_resource_type() const {