### 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)
r_property = default_layer->get_z_index();
			return true;
		} else if (components[1] == "navigation_enabled") {
			r_property = default_layer->is_navigation_enabled();
			return true;
		}
	}
	return false;
}
Vector2 TileMap::map_to_local(const Vector2i &p_pos) const {
	
	ERR_FAIL_COND_V(!tile_set.is_valid(), Vector2());
	Vector2 ret = p_pos;
	TileSet::TileShape tile_shape = tile_set->get_tile_shape();
	TileSet::TileOffsetAxis tile_offset_axis = tile_set->get_tile_offset_axis();
	if (tile_shape == TileSet::TILE_SHAPE_HALF_OFFSET_SQUARE || tile_shape == TileSet::TILE_SHAPE_HEXAGON || tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		
		
		if (tile_offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
			switch (tile_set->get_tile_layout()) {
				case TileSet::TILE_LAYOUT_STACKED:
					ret = Vector2(ret.x + (Math::posmod(ret.y, 2) == 0 ? 0.0 : 0.5), ret.y);
					break;
				case TileSet::TILE_LAYOUT_STACKED_OFFSET:
					ret = Vector2(ret.x + (Math::posmod(ret.y, 2) == 1 ? 0.0 : 0.5), ret.y);
					break;
				case TileSet::TILE_LAYOUT_STAIRS_RIGHT:
					ret = Vector2(ret.x + ret.y / 2, ret.y);
					break;
				case TileSet::TILE_LAYOUT_STAIRS_DOWN: