### 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)

String import_id;
	bool has_import_id = false;
	bool created = false;
	if (!material_set.has(p_material)) {
		material_set.insert(p_material);
		created = true;
	}
	if (p_material->has_meta("import_id")) {
		import_id = p_material->get_meta("import_id");
		has_import_id = true;
	} else if (!p_material->get_name().is_empty()) {
		import_id = p_material->get_name();
		has_import_id = true;
	} else {
		import_id = "@MATERIAL:" + itos(material_set.size() - 1);
	}
	if (!material_map.has(import_id)) {
		MaterialData md;