### 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_COND_V_MSG(!tiles.has(p_atlas_coords), 1, vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	return tiles[p_atlas_coords].animation_frames_durations.size();
}
void TileSetAtlasSource::set_tile_animation_frame_duration(const Vector2i p_atlas_coords, int p_frame_index, real_t p_duration) {
	ERR_FAIL_COND_MSG(!tiles.has(p_atlas_coords), vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	ERR_FAIL_INDEX(p_frame_index, (int)tiles[p_atlas_coords].animation_frames_durations.size());
	ERR_FAIL_COND(p_duration <= 0.0);
	tiles[p_atlas_coords].animation_frames_durations[p_frame_index] = p_duration;
	emit_signal(SNAME("changed"));
}
real_t TileSetAtlasSource::get_tile_animation_frame_duration(const Vector2i p_atlas_coords, int p_frame_index) const {