I agree with your assessment. The reference to “box” makes me think it was definitely the container. I also don’t see the codec called MP4, it’s usually spelled out MPEG-4.
".mp4" is just a file extension, the source of the colloquial name for the container. But both the container and the codec are named MPEG-4 and both are colloquially called "MP4."
"Box level" is apparently referring to types of cryptography, "S-boxes are non-linear transformations of a few input bits that provide confusion and P-boxes simply shuffle the input bits around to provide diffusion"[1] The basic function of S-Box[2] is to transform 8 bits input data into 8 bits of secret data using a precomputed look-up-table (LUT). A "permutation box (or P-box) is a method of bit-shuffling used to permute or transpose bits across S-boxes inputs, retaining diffusion while transposing."[3]
Thanks, I really had no idea what he was talking about... fucking movie atoms. I've always hated those things, and the idea of encrypting them makes them even more sadistic.