### 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)
Vector<String> components = String(p_name).split("/", true, 2);
	
	Vector<String> coords_split = components[0].split(":");
	if (coords_split.size() == 2 && coords_split[0].is_valid_int() && coords_split[1].is_valid_int()) {
		Vector2i coords = Vector2i(coords_split[0].to_int(), coords_split[1].to_int());
		if (tiles.has(coords)) {
			if (components.size() >= 2) {
				
				if (components[1] == "size_in_atlas") {
					r_ret = tiles[coords].size_in_atlas;
					return true;
				} else if (components[1] == "next_alternative_id") {
					r_ret = tiles[coords].next_alternative_id;
					return true;
				} else if (components[1] == "animation_columns") {
					r_ret = get_tile_animation_columns(coords);
					return true;
				} else if (components[1] == "animation_separation") {
					r_ret = get_tile_animation_separation(coords);
					return true;
				} else if (components[1] == "animation_speed") {
					r_ret = get_tile_animation_speed(coords);
					return true;
				} else if (components[1] == "animation_mode") {
					r_ret = get_tile_animation_mode(coords);
					return true;
				} else if (components[1] == "animation_frames_count") {
					r_ret = get_tile_animation_frames_count(coords);
					return true;