Ah so. I read over (most of) that thread. Sounds to me like (maybe) they are talking about extending the effective "sleeping length" of a settee by providing a place for feet to extend into when you are sleeping.
If I understand correctly, this would be similar to the "foot wells" that my Olson has for each settee. Our port settee has an aft foot well under the top of the nav. desk, and the starboard side has one that is under a shallow cabinet forward.
Maybe?
Perhaps a "trotter box" is any sort of container, bag, or even an open-ended compartment. I wonder if the person using that term would call the winch handle pockets in a cockpit coming "winch trotter boxes"?