### 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)
Ref<Texture2D> txt = get_texture();
	if (!txt.is_valid()) {
		return Vector2i();
	}
	ERR_FAIL_COND_V(texture_region_size.x <= 0 || texture_region_size.y <= 0, Vector2i());
	Size2i valid_area = txt->get_size() - margins;
	
	Size2i grid_size;
	if (valid_area.x >= texture_region_size.x && valid_area.y >= texture_region_size.y) {
		valid_area -= texture_region_size;
		grid_size = Size2i(1, 1) + valid_area / (texture_region_size + separation);
	}
	return grid_size;
}
bool TileSetAtlasSource::_set(const StringName &p_name, const Variant &p_value) {
	Vector<String> components = String(p_name).split("/", true, 2);
	
	Vector<String> coords_split = components[0].split(":");
	Vector2i coords = TileSetSource::INVALID_ATLAS_COORDS;
	if (coords_split.size() == 2 && coords_split[0].is_valid_int() && coords_split[1].is_valid_int()) {
		coords = Vector2i(coords_split[0].to_int(), coords_split[1].to_int());
	}
	
	if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
		
		if (!has_tile(coords)) {
			create_tile(coords);
		}
		if (components.size() >= 2) {