### 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)
ERR_FAIL_INDEX(p_terrain_set, terrain_sets.size());
	ERR_FAIL_INDEX(p_terrain_index, terrain_sets[p_terrain_set].terrains.size());
	terrain_sets.write[p_terrain_set].terrains.write[p_terrain_index].name = p_name;
	emit_changed();
}
String TileSet::get_terrain_name(int p_terrain_set, int p_terrain_index) const {
	ERR_FAIL_INDEX_V(p_terrain_set, terrain_sets.size(), String());
	ERR_FAIL_INDEX_V(p_terrain_index, terrain_sets[p_terrain_set].terrains.size(), String());
	return terrain_sets[p_terrain_set].terrains[p_terrain_index].name;
}
void TileSet::set_terrain_color(int p_terrain_set, int p_terrain_index, Color p_color) {
	ERR_FAIL_INDEX(p_terrain_set, terrain_sets.size());
	ERR_FAIL_INDEX(p_terrain_index, terrain_sets[p_terrain_set].terrains.size());
	if (p_color.a != 1.0) {
		WARN_PRINT("Terrain color should have alpha == 1.0");
		p_color.a = 1.0;
	}
	terrain_sets.write[p_terrain_set].terrains.write[p_terrain_index].color = p_color;
	emit_changed();
}
Color TileSet::get_terrain_color(int p_terrain_set, int p_terrain_index) const {
	ERR_FAIL_INDEX_V(p_terrain_set, terrain_sets.size(), Color());
	ERR_FAIL_INDEX_V(p_terrain_index, terrain_sets[p_terrain_set].terrains.size(), Color());
	return terrain_sets[p_terrain_set].terrains[p_terrain_index].color;
}
bool TileSet::is_valid_terrain_peering_bit_for_mode(TileSet::TerrainMode p_terrain_mode, TileSet::CellNeighbor p_peering_bit) const {