### 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(EditorScenePostImport, RefCounted);
	String source_file;
protected:
	static void _bind_methods();
	GDVIRTUAL1R(Object *, _post_import, Node *)
public:
	String get_source_file() const;
	virtual Node *post_import(Node *p_scene);
	virtual void init(const String &p_source_file);
	EditorScenePostImport();
};
class EditorScenePostImportPlugin : public RefCounted {
	GDCLASS(EditorScenePostImportPlugin, RefCounted);
public:
	enum InternalImportCategory {
		INTERNAL_IMPORT_CATEGORY_NODE,
		INTERNAL_IMPORT_CATEGORY_MESH_3D_NODE,
		INTERNAL_IMPORT_CATEGORY_MESH,
		INTERNAL_IMPORT_CATEGORY_MATERIAL,
		INTERNAL_IMPORT_CATEGORY_ANIMATION,
		INTERNAL_IMPORT_CATEGORY_ANIMATION_NODE,
		INTERNAL_IMPORT_CATEGORY_SKELETON_3D_NODE,
		INTERNAL_IMPORT_CATEGORY_MAX
	};
private: