### 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 (has_source(a[0]) && get_source(a[0])->has_tile(a[1]) && get_source(a[0])->has_alternative_tile(a[1], a[2])) {
			alternative_to_remove.push_back(a);
		}
	}
	for (int i = 0; i < alternative_to_remove.size(); i++) {
		Array a = alternative_to_remove[i];
		remove_alternative_level_tile_proxy(a[0], a[1], a[2]);
	}
}
void TileSet::clear_tile_proxies() {
	source_level_proxies.clear();
	coords_level_proxies.clear();
	alternative_level_proxies.clear();
	emit_changed();
}
int TileSet::add_pattern(Ref<TileMapPattern> p_pattern, int p_index) {
	ERR_FAIL_COND_V(!p_pattern.is_valid(), -1);
	ERR_FAIL_COND_V_MSG(p_pattern->is_empty(), -1, "Cannot add an empty pattern to the TileSet.");
	for (const Ref<TileMapPattern> &pattern : patterns) {
		ERR_FAIL_COND_V_MSG(pattern == p_pattern, -1, "TileSet has already this pattern.");
	}
	ERR_FAIL_COND_V(p_index > (int)patterns.size(), -1);
	if (p_index < 0) {
		p_index = patterns.size();
	}
	patterns.insert(p_index, p_pattern);
	emit_changed();
	return p_index;
}
Ref<TileMapPattern> TileSet::get_pattern(int p_index) {