### 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)

const String &src_path = p_source_file;
	Ref<EditorSceneFormatImporter> importer;
	String ext = src_path.get_extension().to_lower();
	EditorProgress progress("import", TTR("Import Scene"), 104);
	progress.step(TTR("Importing Scene..."), 0);
	for (Ref<EditorSceneFormatImporter> importer_elem : importers) {
		List<String> extensions;
		importer_elem->get_extensions(&extensions);
		for (const String &F : extensions) {
			if (F.to_lower() == ext) {
				importer = importer_elem;
				break;
			}
		}
		if (importer.is_valid()) {
			break;
		}
	}
	ERR_FAIL_COND_V(!importer.is_valid(), ERR_FILE_UNRECOGNIZED);
	int import_flags = 0;
	if (animation_importer) {
		import_flags |= EditorSceneFormatImporter::IMPORT_ANIMATION;
		import_flags |= EditorSceneFormatImporter::IMPORT_DISCARD_MESHES_AND_MATERIALS;
	} else {
		if (bool(p_options["animation/import"])) {
			import_flags |= EditorSceneFormatImporter::IMPORT_ANIMATION;