### 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)
for (KeyValue<int, CompatibilityTileData *> &E : compatibility_data) {
		CompatibilityTileData *ctd = E.value;
		
		TileSetAtlasSource *atlas_source = memnew(TileSetAtlasSource);
		int source_id = add_source(Ref<TileSetSource>(atlas_source));
		atlas_source->set_texture(ctd->texture);
		
		switch (ctd->tile_mode) {
			case COMPATIBILITY_TILE_MODE_SINGLE_TILE: {
				atlas_source->set_margins(ctd->region.get_position());
				atlas_source->set_texture_region_size(ctd->region.get_size());
				Vector2i coords;
				for (int flags = 0; flags < 8; flags++) {
					bool flip_h = flags & 1;
					bool flip_v = flags & 2;
					bool transpose = flags & 4;
					Transform2D xform;
					xform = flip_h ? xform.scaled(Size2(-1, 1)) : xform;
					xform = flip_v ? xform.scaled(Size2(1, -1)) : xform;
					xform = transpose ? Transform2D(xform[1], xform[0], Vector2()) : xform;
					int alternative_tile = 0;
					if (!atlas_source->has_tile(coords)) {
						atlas_source->create_tile(coords);
					} else {
						alternative_tile = atlas_source->create_alternative_tile(coords);
					}
					
					Array key_array;
					key_array.push_back(flip_h);