Toe-in is the main parameter that the tie rod ends adjust, but they also need to be adjusted evenly left to right to maintain the correct straight ahead position of the rack. The alignment shop may have assumed that your steering wheel was in the correct position and worked with that.
You can set your steering wheel correctly before taking it back to the shop. Jack up the car and take the front wheels off so that you'll get full steering travel without the tyres fouling anything. Turn the steering wheel lock to lock taking note of exactly how many turns, then turn the wheel half this amount from one lock. This is the correct centre position for the wheel. If it's not centred, take it off and refit it correctly. Then to test, take note of the steering wheel position at both locks, it should be the same offset from centre but opposite direction side to side, ie. you should count the same amount of turns either way from centre.
Hope this makes some semblance of sense!!