In 1953, the projectionist was a skilled professional and not a candy stand attendee thrown in the booth. For the most part, they would center the image based on the main titles and let it go from there. If he noticed heads getting clipped, he could easily rack the framing to adjust. But you're right, this would have to be done with each show.
Regarding the 3-D shorts, after finally watching this set, I'm sorry to say they are terrible. I'm quite familiar with how good they CAN look - both in their original dual-strip Polaroid and the red/blue anaglyph conversions created in the late 60's - and these new cyan/magenta transfers are horrible. Not only is there severe ghosting (double-image) on the magenta eye, but the amount of "noise" is ridiculous. I don't know if it's some form of pixelization or digital artifacting, but it shouldn't be there.
Both shorts were extremely well photographed by Lester H. White and Henry Feulich and this is a far cry from how good these can look in 3-D