No: they are often obstacles, but they've been obstacles since the 19th century, so we have adapted the city and forgotten.
They are often lesser obstacles, since they were built when all other traffic was on foot or by horse, and routes for people had to be maintained. Some motorways were built without this consideration, in the period of 20th century motorcar idealism.
There are more level-crossings, which are less of an impediment since traffic is much less constant on railways. Similarly, there tend to be a lot of under and over passes. These are generally easier since railways are less wide than roads.
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.
With the removal of level crossings (not always replaced with an over or underpass) to make the route suitable for higher-speed trains, railway lines are becoming more of a barrier. But they're still narrower than motorways.
They are often lesser obstacles, since they were built when all other traffic was on foot or by horse, and routes for people had to be maintained. Some motorways were built without this consideration, in the period of 20th century motorcar idealism.