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Depends if you're talking scale or traditional size. They should be fine mixed in with Lionel 6400s.
Gilly
Williams boxcars are similar to MTH Railking boxcars in size. both are larger than Lionel traditional size boxcars. But on real deal railroads boxcars come in different sizes.
From watching countless train videos over the years, you will see boxcars of differing size running together. If the size difference looks too strange, you can break up the profile of the train by placing low-profile cars, like flatcars or gondolas, between the two different-sized boxcars. That way, the size difference is less noticable. That is how I often sneak a traditional-sized car into my otherwise scale consists.
Andy
Watch some 60's era railroad videos and the 'house' cars (box) are all different sizes.....even earlier the difference between a PRR X-29 and a then new box car was noticeable. I'd never run a Lionel 'baby ruth' baby size box car with a scale car....but slight size difference is correct.