### 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)

#include "resource_importer_scene.h"
#include "core/error/error_macros.h"
#include "core/io/resource_saver.h"
#include "editor/editor_node.h"
#include "editor/import/scene_import_settings.h"
#include "scene/3d/area_3d.h"
#include "scene/3d/collision_shape_3d.h"
#include "scene/3d/importer_mesh_instance_3d.h"
#include "scene/3d/mesh_instance_3d.h"
#include "scene/3d/navigation_region_3d.h"
#include "scene/3d/occluder_instance_3d.h"
#include "scene/3d/physics_body_3d.h"
#include "scene/3d/vehicle_body_3d.h"
#include "scene/animation/animation_player.h"
#include "scene/resources/animation.h"
#include "scene/resources/box_shape_3d.h"
#include "scene/resources/importer_mesh.h"
#include "scene/resources/packed_scene.h"
#include "scene/resources/resource_format_text.h"
#include "scene/resources/separation_ray_shape_3d.h"
#include "scene/resources/sphere_shape_3d.h"
#include "scene/resources/surface_tool.h"
#include "scene/resources/world_boundary_shape_3d.h"
uint32_t EditorSceneFormatImporter::get_import_flags() const {