### 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)

} else if (_teststr(name, "navmesh") && Object::cast_to<ImporterMeshInstance3D>(p_node)) {
		if (isroot) {
			return p_node;
		}
		ImporterMeshInstance3D *mi = Object::cast_to<ImporterMeshInstance3D>(p_node);
		Ref<ImporterMesh> mesh = mi->get_mesh();
		ERR_FAIL_COND_V(mesh.is_null(), nullptr);
		NavigationRegion3D *nmi = memnew(NavigationRegion3D);
		nmi->set_name(_fixstr(name, "navmesh"));
		Ref<NavigationMesh> nmesh = mesh->create_navigation_mesh();
		nmi->set_navigation_mesh(nmesh);
		Object::cast_to<Node3D>(nmi)->set_transform(mi->get_transform());
		p_node->replace_by(nmi);
		memdelete(p_node);
		p_node = nmi;
	} else if (_teststr(name, "occ") || _teststr(name, "occonly")) {
		if (isroot) {
			return p_node;
		}
		ImporterMeshInstance3D *mi = Object::cast_to<ImporterMeshInstance3D>(p_node);
		if (mi) {
			Ref<ImporterMesh> mesh = mi->get_mesh();
			if (mesh.is_valid()) {
				if (r_occluder_arrays) {
					OccluderInstance3D::bake_single_node(mi, 0.0f, r_occluder_arrays->first, r_occluder_arrays->second);
				}
				if (_teststr(name, "occ")) {
					String fixed_name = _fixstr(name, "occ");
					if (!fixed_name.is_empty()) {
						if (mi->get_parent() && !mi->get_parent()->has_node(fixed_name)) {