### 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)

if (!p_node) {
		return;
	}
	Node3D *node_3d = Object::cast_to<Node3D>(p_node);
	if (node_3d) {
		p_dictionary.node_3ds.insert(node_3d);
		ImporterMeshInstance3D *mesh_instance_3d = Object::cast_to<ImporterMeshInstance3D>(p_node);
		if (mesh_instance_3d) {
			Ref<ImporterMesh> mesh = mesh_instance_3d->get_mesh();