### 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)
tile_layout = p_layout;
	emit_changed();
}
TileSet::TileLayout TileSet::get_tile_layout() const {
	return tile_layout;
}
void TileSet::set_tile_offset_axis(TileSet::TileOffsetAxis p_alignment) {
	tile_offset_axis = p_alignment;
	for (KeyValue<int, Ref<TileSetSource>> &E_source : sources) {
		E_source.value->notify_tile_data_properties_should_change();
	}
	terrain_bits_meshes_dirty = true;
	tile_meshes_dirty = true;
	emit_changed();
}
TileSet::TileOffsetAxis TileSet::get_tile_offset_axis() const {
	return tile_offset_axis;
}
void TileSet::set_tile_size(Size2i p_size) {
	ERR_FAIL_COND(p_size.x < 1 || p_size.y < 1);
	tile_size = p_size;
	terrain_bits_meshes_dirty = true;
	tile_meshes_dirty = true;
	emit_changed();
}
Size2i TileSet::get_tile_size() const {
	return tile_size;
}
int TileSet::get_next_source_id() const {