### 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)

ERR_FAIL_NULL_MSG(mesh, "Cannot generate shape list with null mesh value");
	ERR_FAIL_NULL_MSG(mesh->get_mesh(), "Cannot generate shape list with null mesh value");
	if (!p_convex) {
		Ref<ConcavePolygonShape3D> shape = mesh->create_trimesh_shape();
		r_shape_list.push_back(shape);
	} else {
		Vector<Ref<Shape3D>> cd;
		cd.push_back(mesh->get_mesh()->create_convex_shape(true,  false));
		if (cd.size()) {
			for (int i = 0; i < cd.size(); i++) {
				r_shape_list.push_back(cd[i]);
			}
		}
	}
}
struct ScalableNodeCollection {
	HashSet<Node3D *> node_3ds;
	HashSet<Ref<ImporterMesh>> importer_meshes;
	HashSet<Ref<Skin>> skins;
	HashSet<Ref<Animation>> animations;
};
void _rescale_importer_mesh(Vector3 p_scale, Ref<ImporterMesh> p_mesh, bool is_shadow = false) {