### 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)
ERR_FAIL_COND_MSG(!tiles.has(p_atlas_coords), vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	TileAlternativesData &tad = tiles[p_atlas_coords];
	for (int frame = 0; frame < (int)tad.animation_frames_durations.size(); frame++) {
		Vector2i frame_coords = p_atlas_coords + (tad.size_in_atlas + tad.animation_separation) * ((tad.animation_columns > 0) ? Vector2i(frame % tad.animation_columns, frame / tad.animation_columns) : Vector2i(frame, 0));
		for (int x = 0; x < tad.size_in_atlas.x; x++) {
			for (int y = 0; y < tad.size_in_atlas.y; y++) {
				Vector2i coords = frame_coords + Vector2i(x, y);
				if (_coords_mapping_cache.has(coords)) {
					WARN_PRINT(vformat("The cache already has a tile for position %s, the position cache might be corrupted.", coords));
				}
				_coords_mapping_cache[coords] = p_atlas_coords;
			}
		}
	}
}
void TileSetAtlasSource::_queue_update_padded_texture() {