### 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)
return separation;
}
void TileSetAtlasSource::set_texture_region_size(Vector2i p_tile_size) {
	if (p_tile_size.x <= 0 || p_tile_size.y <= 0) {
		WARN_PRINT("Atlas source tile_size should be strictly positive.");
		texture_region_size = Vector2i(MAX(1, p_tile_size.x), MAX(1, p_tile_size.y));
	} else {
		texture_region_size = p_tile_size;
	}
	_queue_update_padded_texture();
	emit_changed();
}
Vector2i TileSetAtlasSource::get_texture_region_size() const {
	return texture_region_size;
}
void TileSetAtlasSource::set_use_texture_padding(bool p_use_padding) {
	if (use_texture_padding == p_use_padding) {
		return;
	}
	use_texture_padding = p_use_padding;
	_queue_update_padded_texture();
	emit_changed();
}
bool TileSetAtlasSource::get_use_texture_padding() const {
	return use_texture_padding;
}
Vector2i TileSetAtlasSource::get_atlas_grid_size() const {