Sorry all, my first effort was not complete when I accidentally hit the "send" button.
"The recent issue of Trains Magazine has a number of articles on the shipment of automobiles via rail but is a bit vague about the timeline for the use of box cars."
The article is not only vague on that timeline, but also fails to mention the use of the Evans Auto~Loader or the NYC Railroad's two designs of auto loaders. Though it is not my intent to critique author Peter Hansen, I will state that to ignore the significance of these loading systems, coupled with their impact upon the shipment of finished automobiles and light trucks, is to ignore a, if not the, major factor within the railroads' transport of motor vehicles from 1933 thru the mid 1960's.
I will note (again) that early shipping methods, even when utilizing 36' foot box cars prior to the mass purchases of double door auto cars, routinely employed methods which allowed for four (or more) vehicles to be loaded within cars. Double decking and tilting cars in much the same manner as the future auto loaders was common place and essential in order to meet minimum weights specified within tariffs. It must be borne in mind that an average automobile produced in the 'teens weighed less than a ton. Ford; not alone in shipping multiple vehicles, whether knocked down or complete, didn't require a fifty ton automobile car to transport his product.
"It has been my understanding -- perhaps misguided -- that automobile shipments after WWII moved from rail to highway over the road trailer and very few cars were shipped in box cars at this time period."
Railroads lost the majority share of new, fully assembled, auto and light truck shipments to trucking in 1932, and never recaptured that advantage until after 1960. Prior to the 1930's, shipments of automobiles and light trucks were dominated by the railroads. In 1932 51.5% of new autos and light trucks were delivered by truck or so-called "drive-aways"-- the latter two methods of delivery were grouped statistically (during that period), thus it is hard to derive the true percentage hauled by truck.
None-the less, the railroads maintained an average of around 40% of the finished motor vehicle traffic during the pre-war years. When auto production resumed in 1945 the railroads continued a down hill slide in shipments due in part to; equipment in disrepair, manufacturers operating more regional assembly plants and rate wars with trucking interests.
"1) is my understanding of the shipment of automobiles via rail correct?"
No, the railroads still handled a good portion of the automobile and light truck traffic during the post war years from which they received a higher profit per ton than virtually any other commodity.
"2) were automobiles being shipped in box cars into the 1950's?"
Yes, by the thousands.
"3) if YES, then what makes were shipped by rail?"
Ford, Lincoln, Mercury, Chevrolet, Pontiac, Buick, Oldsmobile, Cadillac, Chrysler, Dodge, Plymouth, Checker, DeSoto, Hudson, Kaiser, Nash, Packard, Studebaker, Willys and Crosley.
"4) after WWII was box car shipment of automobiles, if shipped in a box car, done using 40-foot or 50-foot box cars?"
40-foot auto cars equipped with Evans Auto~Loaders outnumbered 50-foot auto cars (so equipped) until mid-1957. For your year of interest; 1953, there were well over 18.000 40-foot cars and around 11,000 50-footers. 40-foot cars were as well suited as their 50-foot companions when small to mid-sized vehicles were shipped.
50-foot cars were purchased in large part to serve the small truck market as well as autos. The racks were equipped with wide wheel pans which allowed either automobiles or trucks to be loaded. The extra length coupled with generally (at least) a 10' 6" inside height allowed larger, and longer vehicles to be more easily positioned on the floor of the car once the vehicle placed on the rack had been raised and secured for shipment. A common load for such cars was two automobiles placed on the racks and two light trucks placed on the floor. Also, a good percentage of 50-foot cars were equipped with Type "F" loaders (with sixteen floor tubes) which along with Evans final model, the Type "G" could accommodate five automobiles.