Remember that each builders car was probably slightly different. And many RRs built their own cars.
Basically on the prototypes, the bolster would probably be about the same height, but the roof line could be anywhere. For example an X-29 has a 9 1/2 ft inside height while a 1937 ara car has a 10 1/2 ft inside height. So before you panic too much, you might want to check on the prototypes.
One thing to note is that Atlas cars originally had very wide trucks. That tended to not look right to many people. Atlas has changed that in recent years but the old ones are still out there.
Another note is that Atlas as is typical of 3-rail focused manufacturers uses a truck mounting system that is unique to their product. Lionel and MTH do the same. All 3 make it a project to replace the trucks with another brand.
To replace trucks, it is generally easier to also replace the body bolster on the car. Cars made by 2-rail focused mfg tend to use standard bolster height.
The good news is we still get some nice models that are worth converting.
I personally have been able to live with the too-wide trucks. They roll well and it is not so noticable from 3 feet away. I have too many other projects to worry about it now.