### 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)
Ref<Texture2D> tex = atlas_source->get_runtime_texture();
		if (!tex.is_valid()) {
			return;
		}
		
		Vector2i grid_size = atlas_source->get_atlas_grid_size();
		if (p_atlas_coords.x >= grid_size.x || p_atlas_coords.y >= grid_size.y) {
			return;
		}
		
		const TileData *tile_data = p_tile_data_override ? p_tile_data_override : atlas_source->get_tile_data(p_atlas_coords, p_alternative_tile);
		
		Color modulate = tile_data->get_modulate() * p_modulation;
		
		Vector2 tile_offset = tile_data->get_texture_origin();
		
		Rect2 dest_rect;
		dest_rect.size = atlas_source->get_runtime_tile_texture_region(p_atlas_coords).size;
		dest_rect.size.x += FP_ADJUST;
		dest_rect.size.y += FP_ADJUST;
		bool transpose = tile_data->get_transpose() ^ bool(p_alternative_tile & TileSetAtlasSource::TRANSFORM_TRANSPOSE);
		if (transpose) {
			dest_rect.position = (p_position - Vector2(dest_rect.size.y, dest_rect.size.x) / 2 - tile_offset);
		} else {
			dest_rect.position = (p_position - dest_rect.size / 2 - tile_offset);
		}
		if (tile_data->get_flip_h() ^ bool(p_alternative_tile & TileSetAtlasSource::TRANSFORM_FLIP_H)) {
			dest_rect.size.x = -dest_rect.size.x;
		}