### 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), Rect2i(), vformat("TileSetAtlasSource has no tile at %s.", String(p_atlas_coords)));
	ERR_FAIL_INDEX_V(p_frame, (int)tiles[p_atlas_coords].animation_frames_durations.size(), Rect2i());
	const TileAlternativesData &tad = tiles[p_atlas_coords];
	Vector2i size_in_atlas = tad.size_in_atlas;
	Vector2 region_size = texture_region_size * size_in_atlas + separation * (size_in_atlas - Vector2i(1, 1));
	Vector2i frame_coords = p_atlas_coords + (size_in_atlas + tad.animation_separation) * ((tad.animation_columns > 0) ? Vector2i(p_frame % tad.animation_columns, p_frame / tad.animation_columns) : Vector2i(p_frame, 0));
	Vector2 origin = margins + (frame_coords * (texture_region_size + separation));
	return Rect2(origin, region_size);
}
bool TileSetAtlasSource::is_position_in_tile_texture_region(const Vector2i p_atlas_coords, int p_alternative_tile, Vector2 p_position) const {