Scale means the item is based on the real thing with all dimensions reduced to model size. For O scale, our models are 1/48 of full size. This works out to be 1/4 inch to the foot, referred to as 1/4 inch scale. For example, a standard real 40 foot long boxcar, is 40 ft long over the end sills. Since in our scale 1/4 inch equals a foot, a scale model of that car should be 40 x 1/4 inches or 10 inches long. All dimensions can generally be found for the real cars.
The Pennsy X43 boxcar is close to most of the newer 40 ft cars. it is supposed to be 40 5 1/16 inches inside. The overall height about the rails should be 15 ft 7/32 inch. the width should be 9 feet 9 5/8 inches. An accurate model would be a 10 1/8 inches long, 3 3/4 inches above the rails, and 2 1/2 inches wide. There are diagrams with major dimensions for PRR cars on the a Website prr.railfan.net. Also remember there are many types of 40ft boxcars and other prototypes would be different, especially in the height.
Many of the lower priced cars such as the rail king line, Atlas industrical rail, and Lionel 027, are made made smaller than scale. some much smaller. Many of the locos are undersized too, but they sorta match the cars. The frustrating part is that they don't always compress the dimensions by the same amount. if they did, it would all be to the same scale whatever that is and would look good together. And some just do strange stuff. The old Lionel 6464 boxcars were sorta based on a real 40 ft car and were about 10 inches long. But they were way too narrow, and too low.
The one thing that really shocked me was when I first saw a full O scale model of the PRR steam Turbine. I was familiar with the lionel model which is about the size of the midrange lionel steamers. I saw this brass scale one and it was gigantic! it must have been twice as long, and twice as tall. the tender was much much bigger. Of course the lionel one was made to go around 31 inch diameter curves, while the scale one (still o gauge) would probably need about 10 foot diameter curves.
Generally the scale models do cost a little more. the old Weaver Line, was pretty inexpensive, and was all scale. this is the lionel "lionscale" line now I think. I think they bought all the weaver molds.