### 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 ((p_from_layout == TileSet::TILE_LAYOUT_STAIRS_RIGHT) ^ (p_offset_axis == TileSet::TILE_OFFSET_AXIS_VERTICAL)) {
				if (output.y < 0 && bool(output.y % 2)) {
					output = Vector2i(output.x + output.y / 2 - 1, output.y);
				} else {
					output = Vector2i(output.x + output.y / 2, output.y);
				}
			} else {
				if (output.x < 0 && bool(output.x % 2)) {
					output = Vector2i(output.x / 2 - 1, output.x + output.y * 2);
				} else {
					output = Vector2i(output.x / 2, output.x + output.y * 2);
				}
			}
			break;
		case TileSet::TILE_LAYOUT_DIAMOND_RIGHT:
		case TileSet::TILE_LAYOUT_DIAMOND_DOWN:
			if ((p_from_layout == TileSet::TILE_LAYOUT_DIAMOND_RIGHT) ^ (p_offset_axis == TileSet::TILE_OFFSET_AXIS_VERTICAL)) {
				if ((output.x + output.y) < 0 && (output.x - output.y) % 2) {
					output = Vector2i((output.x + output.y) / 2 - 1, output.y - output.x);
				} else {
					output = Vector2i((output.x + output.y) / 2, -output.x + output.y);
				}
			} else {
				if ((output.x - output.y) < 0 && (output.x + output.y) % 2) {
					output = Vector2i((output.x - output.y) / 2 - 1, output.x + output.y);
				} else {
					output = Vector2i((output.x - output.y) / 2, output.x + output.y);
				}
			}
			break;