When I bought the Phoebe Snow Refer Car, I saw O gauge on the box and I thought that it would match my Lionel # 731 Set cars perfectly but after putting the car in the set I quickly saw the difference in size with the rest of the cars, especially the New Haven Box Car.
Is this the car you have, K762-1471?
If so it was made about 50 years after your 6468 box car. Why would you expect a 50 year old toy to perfectly match something made 50 years later by another company?
Can anyone explain to me how you figure these scale ratios out?
Sure
If you buy Atlas Master Line, Atlas Trainman, Lionel Standard O or MTH Premier you will be buying a 1:48 scale model. If you buy something else you may be buying a 1:48 scale model, a scale model of some other ratio, a toy that has been "selectively compressed" from a real world prototype or simply a toy based on nothing more than the designers imagination and sense of what looked appealing to children or the parents who bought toys for them.
If you decide to go the all 1:48 scale route you should be aware that real world freight cars, even box cars and reefers, were never made to perfectly match each other. 
