### 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)
Array from;
	from.push_back(p_source_from);
	from.push_back(p_coords_from);
	ERR_FAIL_COND(!coords_level_proxies.has(from));
	coords_level_proxies.erase(from);
	emit_changed();
}
void TileSet::set_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from, int p_source_to, Vector2i p_coords_to, int p_alternative_to) {
	ERR_FAIL_COND(p_source_from == TileSet::INVALID_SOURCE || p_source_to == TileSet::INVALID_SOURCE);
	ERR_FAIL_COND(p_coords_from == TileSetSource::INVALID_ATLAS_COORDS || p_coords_to == TileSetSource::INVALID_ATLAS_COORDS);
	Array from;
	from.push_back(p_source_from);
	from.push_back(p_coords_from);
	from.push_back(p_alternative_from);
	Array to;
	to.push_back(p_source_to);
	to.push_back(p_coords_to);
	to.push_back(p_alternative_to);
	alternative_level_proxies[from] = to;
	emit_changed();
}
Array TileSet::get_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from) {
	Array from;
	from.push_back(p_source_from);
	from.push_back(p_coords_from);
	from.push_back(p_alternative_from);
	ERR_FAIL_COND_V(!alternative_level_proxies.has(from), Array());
	return alternative_level_proxies[from];
}
bool TileSet::has_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from) {