### 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<EditorScenePostImport> post_import_script;
	if (!post_import_script_path.is_empty()) {
		Ref<Script> scr = ResourceLoader::load(post_import_script_path);
		if (!scr.is_valid()) {
			EditorNode::add_io_error(TTR("Couldn't load post-import script:") + " " + post_import_script_path);
		} else {
			post_import_script = Ref<EditorScenePostImport>(memnew(EditorScenePostImport));
			post_import_script->set_script(scr);
			if (!post_import_script->get_script_instance()) {
				EditorNode::add_io_error(TTR("Invalid/broken script for post-import (check console):") + " " + post_import_script_path);
				post_import_script.unref();
				return ERR_CANT_CREATE;
			}
		}
	}
	if (post_import_script.is_valid()) {
		post_import_script->init(p_source_file);
		scene = post_import_script->post_import(scene);
		if (!scene) {
			EditorNode::add_io_error(
					TTR("Error running post-import script:") + " " + post_import_script_path + "\n" +
					TTR("Did you return a Node-derived object in the `_post_import()` method?"));
			return err;
		}
	}
	for (int i = 0; i < post_importer_plugins.size(); i++) {
		post_importer_plugins.write[i]->post_process(scene, p_options);
	}
	progress.step(TTR("Saving..."), 104);
	if (animation_importer) {