### 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 "tile_map.h"
#include "tile_map.compat.inc"
#include "core/core_string_names.h"
#include "core/io/marshalls.h"
#include "scene/resources/world_2d.h"
#include "servers/navigation_server_2d.h"
#ifdef DEBUG_ENABLED
#include "servers/navigation_server_3d.h"
#endif 
#ifdef DEBUG_ENABLED
constexpr int TILE_MAP_DEBUG_QUADRANT_SIZE = 16;
Vector2i TileMapLayer::_coords_to_debug_quadrant_coords(const Vector2i &p_coords) const {
	return Vector2i(
			p_coords.x > 0 ? p_coords.x / TILE_MAP_DEBUG_QUADRANT_SIZE : (p_coords.x - (TILE_MAP_DEBUG_QUADRANT_SIZE - 1)) / TILE_MAP_DEBUG_QUADRANT_SIZE,
			p_coords.y > 0 ? p_coords.y / TILE_MAP_DEBUG_QUADRANT_SIZE : (p_coords.y - (TILE_MAP_DEBUG_QUADRANT_SIZE - 1)) / TILE_MAP_DEBUG_QUADRANT_SIZE);
}
void TileMapLayer::_debug_update() {