### 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)
if (!tile_set.is_valid()) {
		return;
	}
	
	Vector2i tile_size = tile_set->get_tile_size();
	Vector<Vector2> polygon = tile_set->get_tile_shape_polygon();
	TileSet::TileShape shape = tile_set->get_tile_shape();
	for (const Vector2i &E : p_cells) {
		Vector2 center = map_to_local(E);
#define DRAW_SIDE_IF_NEEDED(side, polygon_index_from, polygon_index_to)                     \
	if (!p_cells.has(get_neighbor_cell(E, side))) {                                         \
		Vector2 from = p_transform.xform(center + polygon[polygon_index_from] * tile_size); \
		Vector2 to = p_transform.xform(center + polygon[polygon_index_to] * tile_size);     \
		p_control->draw_line(from, to, p_color);                                            \
	}
		if (shape == TileSet::TILE_SHAPE_SQUARE) {
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_RIGHT_SIDE, 1, 2);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_SIDE, 2, 3);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_LEFT_SIDE, 3, 0);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_SIDE, 0, 1);
		} else if (shape == TileSet::TILE_SHAPE_ISOMETRIC) {
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE, 2, 3);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE, 1, 2);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE, 0, 1);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE, 3, 0);
		} else {
			if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE, 3, 4);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE, 2, 3);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_LEFT_SIDE, 1, 2);