### 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)
class TileSetSource;
class TileSetAtlasSource;
class TileData;
class TileSetPlugin;
class TileSetPluginAtlasRendering;
class TileSetPluginAtlasPhysics;
class TileSetPluginAtlasNavigation;
union TileMapCell {
	struct {
		int16_t source_id;
		int16_t coord_x;
		int16_t coord_y;
		int16_t alternative_tile;
	};
	uint64_t _u64t;
	static uint32_t hash(const TileMapCell &p_hash) {
		return hash_one_uint64(p_hash._u64t);
	}
	TileMapCell(int p_source_id = -1, Vector2i p_atlas_coords = Vector2i(-1, -1), int p_alternative_tile = -1) { 
		source_id = p_source_id;
		set_atlas_coords(p_atlas_coords);
		alternative_tile = p_alternative_tile;
	}
	Vector2i get_atlas_coords() const {