### 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)
int c = p_data.size();
	const int *r = p_data.ptr();
	int offset = 3;
	ERR_FAIL_COND_MSG(c % offset != 0, "Corrupted tile data.");
	clear();
	for (int i = 0; i < c; i += offset) {
		const uint8_t *ptr = (const uint8_t *)&r[i];
		uint8_t local[12];
		for (int j = 0; j < 12; j++) {
			local[j] = ptr[j];
		}
#ifdef BIG_ENDIAN_ENABLED
		SWAP(local[0], local[3]);
		SWAP(local[1], local[2]);
		SWAP(local[4], local[7]);
		SWAP(local[5], local[6]);
		SWAP(local[8], local[11]);
		SWAP(local[9], local[10]);
#endif
		int16_t x = decode_uint16(&local[0]);
		int16_t y = decode_uint16(&local[2]);
		uint16_t source_id = decode_uint16(&local[4]);
		uint16_t atlas_coords_x = decode_uint16(&local[6]);
		uint16_t atlas_coords_y = decode_uint16(&local[8]);
		uint16_t alternative_tile = decode_uint16(&local[10]);
		set_cell(Vector2i(x, y), source_id, Vector2i(atlas_coords_x, atlas_coords_y), alternative_tile);
	}
	emit_signal(SNAME("changed"));
}
Vector<int> TileMapPattern::_get_tile_data() const {