### 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 (components[1] == "size_in_atlas") {
				move_tile_in_atlas(coords, coords, p_value);
				return true;
			} else if (components[1] == "next_alternative_id") {
				tiles[coords].next_alternative_id = p_value;
				return true;
			} else if (components[1] == "animation_columns") {
				set_tile_animation_columns(coords, p_value);
				return true;
			} else if (components[1] == "animation_separation") {
				set_tile_animation_separation(coords, p_value);
				return true;
			} else if (components[1] == "animation_speed") {
				set_tile_animation_speed(coords, p_value);
				return true;
			} else if (components[1] == "animation_mode") {
				set_tile_animation_mode(coords, VariantCaster<TileSetAtlasSource::TileAnimationMode>::cast(p_value));
				return true;
			} else if (components[1] == "animation_frames_count") {
				set_tile_animation_frames_count(coords, p_value);
				return true;
			} else if (components.size() >= 3 && components[1].begins_with("animation_frame_") && components[1].trim_prefix("animation_frame_").is_valid_int()) {
				int frame = components[1].trim_prefix("animation_frame_").to_int();
				if (components[2] == "duration") {
					if (frame >= get_tile_animation_frames_count(coords)) {
						set_tile_animation_frames_count(coords, frame + 1);
					}
					set_tile_animation_frame_duration(coords, frame, p_value);
					return true;