### 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)
ClassDB::bind_method(D_METHOD("get_next_source_id"), &TileSet::get_next_source_id);
	ClassDB::bind_method(D_METHOD("add_source", "source", "atlas_source_id_override"), &TileSet::add_source, DEFVAL(TileSet::INVALID_SOURCE));
	ClassDB::bind_method(D_METHOD("remove_source", "source_id"), &TileSet::remove_source);
	ClassDB::bind_method(D_METHOD("set_source_id", "source_id", "new_source_id"), &TileSet::set_source_id);
	ClassDB::bind_method(D_METHOD("get_source_count"), &TileSet::get_source_count);
	ClassDB::bind_method(D_METHOD("get_source_id", "index"), &TileSet::get_source_id);
	ClassDB::bind_method(D_METHOD("has_source", "source_id"), &TileSet::has_source);
	ClassDB::bind_method(D_METHOD("get_source", "source_id"), &TileSet::get_source);
	
	ClassDB::bind_method(D_METHOD("set_tile_shape", "shape"), &TileSet::set_tile_shape);
	ClassDB::bind_method(D_METHOD("get_tile_shape"), &TileSet::get_tile_shape);
	ClassDB::bind_method(D_METHOD("set_tile_layout", "layout"), &TileSet::set_tile_layout);
	ClassDB::bind_method(D_METHOD("get_tile_layout"), &TileSet::get_tile_layout);
	ClassDB::bind_method(D_METHOD("set_tile_offset_axis", "alignment"), &TileSet::set_tile_offset_axis);
	ClassDB::bind_method(D_METHOD("get_tile_offset_axis"), &TileSet::get_tile_offset_axis);
	ClassDB::bind_method(D_METHOD("set_tile_size", "size"), &TileSet::set_tile_size);
	ClassDB::bind_method(D_METHOD("get_tile_size"), &TileSet::get_tile_size);
	ADD_PROPERTY(PropertyInfo(Variant::INT, "tile_shape", PROPERTY_HINT_ENUM, "Square,Isometric,Half-Offset Square,Hexagon"), "set_tile_shape", "get_tile_shape");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "tile_layout", PROPERTY_HINT_ENUM, "Stacked,Stacked Offset,Stairs Right,Stairs Down,Diamond Right,Diamond Down"), "set_tile_layout", "get_tile_layout");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "tile_offset_axis", PROPERTY_HINT_ENUM, "Horizontal Offset,Vertical Offset"), "set_tile_offset_axis", "get_tile_offset_axis");
	ADD_PROPERTY(PropertyInfo(Variant::VECTOR2I, "tile_size", PROPERTY_HINT_NONE, "suffix:px"), "set_tile_size", "get_tile_size");
	
	ClassDB::bind_method(D_METHOD("set_uv_clipping", "uv_clipping"), &TileSet::set_uv_clipping);
	ClassDB::bind_method(D_METHOD("is_uv_clipping"), &TileSet::is_uv_clipping);
	ClassDB::bind_method(D_METHOD("get_occlusion_layers_count"), &TileSet::get_occlusion_layers_count);