### 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)

bool save = anim_settings["save_to_file/enabled"];
				String path = anim_settings["save_to_file/path"];
				bool keep_custom = anim_settings["save_to_file/keep_custom_tracks"];
				Ref<Animation> saved_anim = _save_animation_to_file(anim, save, path, keep_custom);
				if (saved_anim != anim) {
					Ref<AnimationLibrary> al = ap->get_animation_library(ap->find_animation_library(anim));
					al->add_animation(name, saved_anim); 
				}
			}
		}
	}
	return p_node;
}
Node *ResourceImporterScene::_post_fix_node(Node *p_node, Node *p_root, HashMap<Ref<ImporterMesh>, Vector<Ref<Shape3D>>> &collision_map, Pair<PackedVector3Array, PackedInt32Array> &r_occluder_arrays, HashSet<Ref<ImporterMesh>> &r_scanned_meshes, const Dictionary &p_node_data, const Dictionary &p_material_data, const Dictionary &p_animation_data, float p_animation_fps) {
	
	for (int i = 0; i < p_node->get_child_count(); i++) {
		Node *r = _post_fix_node(p_node->get_child(i), p_root, collision_map, r_occluder_arrays, r_scanned_meshes, p_node_data, p_material_data, p_animation_data, p_animation_fps);
		if (!r) {
			i--; 
		}
	}
	bool isroot = p_node == p_root;
	String import_id = p_node->get_meta("import_id", "PATH:" + p_root->get_path_to(p_node));
	Dictionary node_settings;
	if (p_node_data.has(import_id)) {
		node_settings = p_node_data[import_id];
	}
	if (!isroot && (node_settings.has("import/skip_import") && bool(node_settings["import/skip_import"]))) {
		memdelete(p_node);
		return nullptr;