"Scale" is definitely a relative term in O-gauge product lines that aren't specifically produced as exact-scale product lines. The other hitch you're running into with MPC-era rolling stock is that it's essentially postwar-era stock that was updated with better painting processes and new or re-introduced details. Postwar Lionel was a mix of scale proportions and "selectively compressed" designs to fit within the limitations of standard "O" and "O-27" track layouts. To be fair, Lionel's selective compression of proportions was generally done with a remarkable level of care and artistry so that it's hard to tell where a model was shortened/reduced unless you set it right next to a full-scale version. They manage to just "look right" as long as you don't disrupt the illusion with a scale model alongside, or a modern selectively-compressed model that's not quite as well-executed as some of the old stuff.
The other thing you're running into is that the typical postwar or MPC boxcar is a model of a mid-20th-century 40-foot boxcar. While they were quite big in their day, they're tiny by modern standards. In real life, modern equipment will dwarf them, especially in height. Clearances have been raised nearly everywhere on US Class 1 railroads, so the lower profiles of older equipment is often due to the then-prevailing height limitations of bridges and tunnels. Generally, the "ride height" of postwar/MPC cars is reasonable (if not a bit high, by true scale measurements) in proportion to the clearance needed for the already-oversized flanges required for tubular track. What you're noticing is that a 1940's-era boxcar does indeed look mis-proportioned in relation to equipment from the later 20th and now 21st century.
