For the section of rail parallel to the tunnel, there is only one grade crossing at Sphinxlunet and one foot crossing in the station. While it is hard to see from satellite view after the tunnel is built, there were likely more crossings at the aforementioned stop lights on A2. Width of right-of-ways is not too important if there is no way to get across the narrower one either.
Most likely the tunnel is really due two conflicting desires - wanting to remove stoplights from the A2 to expedited the flow of through traffic while not wanting to route A2 around the city's east perimeter where there is ample open land. Usually the city retailers and other businesses want to keep the central routing to prevent the development of competing business centers along perimeter highways.