### 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)

MESH_OVERRIDE_DEFAULT,
		MESH_OVERRIDE_ENABLE,
		MESH_OVERRIDE_DISABLE,
	};
	enum BodyType {
		BODY_TYPE_STATIC,
		BODY_TYPE_DYNAMIC,
		BODY_TYPE_AREA
	};
	enum ShapeType {
		SHAPE_TYPE_DECOMPOSE_CONVEX,
		SHAPE_TYPE_SIMPLE_CONVEX,
		SHAPE_TYPE_TRIMESH,
		SHAPE_TYPE_BOX,
		SHAPE_TYPE_SPHERE,
		SHAPE_TYPE_CYLINDER,
		SHAPE_TYPE_CAPSULE,
	};
	Array _get_skinned_pose_transforms(ImporterMeshInstance3D *p_src_mesh_node);
	void _replace_owner(Node *p_node, Node *p_scene, Node *p_new_owner);
	void _generate_meshes(Node *p_node, const Dictionary &p_mesh_data, bool p_generate_lods, bool p_create_shadow_meshes, LightBakeMode p_light_bake_mode, float p_lightmap_texel_size, const Vector<uint8_t> &p_src_lightmap_cache, Vector<Vector<uint8_t>> &r_lightmap_caches);
	void _add_shapes(Node *p_node, const Vector<Ref<Shape3D>> &p_shapes);
	enum AnimationImportTracks {
		ANIMATION_IMPORT_TRACKS_IF_PRESENT,
		ANIMATION_IMPORT_TRACKS_IF_PRESENT_FOR_ALL,
		ANIMATION_IMPORT_TRACKS_NEVER,
	};
	enum TrackChannel {