### 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)

GDCLASS(ResourceImporterScene, ResourceImporter);
	static Vector<Ref<EditorSceneFormatImporter>> importers;
	static Vector<Ref<EditorScenePostImportPlugin>> post_importer_plugins;
	static ResourceImporterScene *scene_singleton;
	static ResourceImporterScene *animation_singleton;
	enum LightBakeMode {
		LIGHT_BAKE_DISABLED,
		LIGHT_BAKE_STATIC,
		LIGHT_BAKE_STATIC_LIGHTMAPS,
		LIGHT_BAKE_DYNAMIC,
	};
	enum MeshPhysicsMode {
		MESH_PHYSICS_DISABLED,
		MESH_PHYSICS_MESH_AND_STATIC_COLLIDER,
		MESH_PHYSICS_RIGID_BODY_AND_MESH,
		MESH_PHYSICS_STATIC_COLLIDER_ONLY,
		MESH_PHYSICS_AREA_ONLY,
	};
	enum NavMeshMode {
		NAVMESH_DISABLED,
		NAVMESH_MESH_AND_NAVMESH,
		NAVMESH_NAVMESH_ONLY,
	};
	enum OccluderMode {
		OCCLUDER_DISABLED,
		OCCLUDER_MESH_AND_OCCLUDER,
		OCCLUDER_OCCLUDER_ONLY,
	};
	enum MeshOverride {