### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
#include "nav_mesh_generator_2d.h"
#include "core/config/project_settings.h"
#include "scene/2d/mesh_instance_2d.h"
#include "scene/2d/multimesh_instance_2d.h"
#include "scene/2d/physics_body_2d.h"
#include "scene/2d/polygon_2d.h"
#include "scene/2d/tile_map.h"
#include "scene/resources/capsule_shape_2d.h"
#include "scene/resources/circle_shape_2d.h"
#include "scene/resources/concave_polygon_shape_2d.h"
#include "scene/resources/convex_polygon_shape_2d.h"
#include "scene/resources/navigation_mesh_source_geometry_data_2d.h"
#include "scene/resources/navigation_polygon.h"
#include "scene/resources/rectangle_shape_2d.h"
#include "thirdparty/clipper2/include/clipper2/clipper.h"
#include "thirdparty/misc/polypartition.h"
NavMeshGenerator2D *NavMeshGenerator2D::singleton = nullptr;
Mutex NavMeshGenerator2D::baking_navmesh_mutex;
Mutex NavMeshGenerator2D::generator_task_mutex;
bool NavMeshGenerator2D::use_threads = true;
bool NavMeshGenerator2D::baking_use_multiple_threads = true;
bool NavMeshGenerator2D::baking_use_high_priority_threads = true;
HashSet<Ref<NavigationPolygon>> NavMeshGenerator2D::baking_navmeshes;
HashMap<WorkerThreadPool::TaskID, NavMeshGenerator2D::NavMeshGeneratorTask2D *> NavMeshGenerator2D::generator_tasks;
NavMeshGenerator2D *NavMeshGenerator2D::get_singleton() {