### 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)
ClassDB::bind_method(D_METHOD("set_tile_animation_speed", "atlas_coords", "speed"), &TileSetAtlasSource::set_tile_animation_speed);
	ClassDB::bind_method(D_METHOD("get_tile_animation_speed", "atlas_coords"), &TileSetAtlasSource::get_tile_animation_speed);
	ClassDB::bind_method(D_METHOD("set_tile_animation_mode", "atlas_coords", "mode"), &TileSetAtlasSource::set_tile_animation_mode);
	ClassDB::bind_method(D_METHOD("get_tile_animation_mode", "atlas_coords"), &TileSetAtlasSource::get_tile_animation_mode);
	ClassDB::bind_method(D_METHOD("set_tile_animation_frames_count", "atlas_coords", "frames_count"), &TileSetAtlasSource::set_tile_animation_frames_count);
	ClassDB::bind_method(D_METHOD("get_tile_animation_frames_count", "atlas_coords"), &TileSetAtlasSource::get_tile_animation_frames_count);
	ClassDB::bind_method(D_METHOD("set_tile_animation_frame_duration", "atlas_coords", "frame_index", "duration"), &TileSetAtlasSource::set_tile_animation_frame_duration);
	ClassDB::bind_method(D_METHOD("get_tile_animation_frame_duration", "atlas_coords", "frame_index"), &TileSetAtlasSource::get_tile_animation_frame_duration);
	ClassDB::bind_method(D_METHOD("get_tile_animation_total_duration", "atlas_coords"), &TileSetAtlasSource::get_tile_animation_total_duration);
	
	ClassDB::bind_method(D_METHOD("create_alternative_tile", "atlas_coords", "alternative_id_override"), &TileSetAtlasSource::create_alternative_tile, DEFVAL(INVALID_TILE_ALTERNATIVE));
	ClassDB::bind_method(D_METHOD("remove_alternative_tile", "atlas_coords", "alternative_tile"), &TileSetAtlasSource::remove_alternative_tile);
	ClassDB::bind_method(D_METHOD("set_alternative_tile_id", "atlas_coords", "alternative_tile", "new_id"), &TileSetAtlasSource::set_alternative_tile_id);
	ClassDB::bind_method(D_METHOD("get_next_alternative_tile_id", "atlas_coords"), &TileSetAtlasSource::get_next_alternative_tile_id);
	ClassDB::bind_method(D_METHOD("get_tile_data", "atlas_coords", "alternative_tile"), &TileSetAtlasSource::get_tile_data);
	
	ClassDB::bind_method(D_METHOD("get_atlas_grid_size"), &TileSetAtlasSource::get_atlas_grid_size);
	ClassDB::bind_method(D_METHOD("get_tile_texture_region", "atlas_coords", "frame"), &TileSetAtlasSource::get_tile_texture_region, DEFVAL(0));
	
	ClassDB::bind_method(D_METHOD("_update_padded_texture"), &TileSetAtlasSource::_update_padded_texture);
	ClassDB::bind_method(D_METHOD("get_runtime_texture"), &TileSetAtlasSource::get_runtime_texture);
	ClassDB::bind_method(D_METHOD("get_runtime_tile_texture_region", "atlas_coords", "frame"), &TileSetAtlasSource::get_runtime_tile_texture_region);
	BIND_ENUM_CONSTANT(TILE_ANIMATION_MODE_DEFAULT)
	BIND_ENUM_CONSTANT(TILE_ANIMATION_MODE_RANDOM_START_TIMES)
	BIND_ENUM_CONSTANT(TILE_ANIMATION_MODE_MAX)
	BIND_CONSTANT(TRANSFORM_FLIP_H)
	BIND_CONSTANT(TRANSFORM_FLIP_V)
	BIND_CONSTANT(TRANSFORM_TRANSPOSE)
}
TileSetAtlasSource::~TileSetAtlasSource() {