### 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)
Array p = p_value;
					Vector2i last_coord;
					while (p.size() > 0) {
						if (p[0].get_type() == Variant::VECTOR2) {
							last_coord = p[0];
						} else if (p[0].get_type() == Variant::INT) {
							ctd->autotile_bitmask_flags.insert(last_coord, p[0]);
						}
						p.pop_front();
					}
				}
			} else if (what == "occluder_map") {
				Array p = p_value;
				Vector2 last_coord;
				while (p.size() > 0) {
					if (p[0].get_type() == Variant::VECTOR2) {
						last_coord = p[0];
					} else if (p[0].get_type() == Variant::OBJECT) {
						ctd->autotile_occluder_map.insert(last_coord, p[0]);
					}
					p.pop_front();
				}
			} else if (what == "navpoly_map") {
				Array p = p_value;
				Vector2 last_coord;
				while (p.size() > 0) {
					if (p[0].get_type() == Variant::VECTOR2) {
						last_coord = p[0];
					} else if (p[0].get_type() == Variant::OBJECT) {
						ctd->autotile_navpoly_map.insert(last_coord, p[0]);