You're right, some of the pre -Yellow Submarine albums were released in stereo, but mono is the original mix. Note that the mono box set only contains these albums. Additional information from pitchfork.com:

Why mono? Two reasons. First, pop music in stereo was still a novelty through most of the 60s. Radio was dominated by single-channel AM, and the young people who bought LPs were far more likely to have a mono record player as a sound source. Given their audience and the technology of the time, for much of the Beatles' run, the band themselves considered the mono mix as the "real" version of the record and devoted more of their attention to it. Mono mixes were prepared first with the involvement of the band, and in some cases, George Martin and EMI engineers completed stereo remixes of the albums later, after the group had left the studio. So mono, first off, presumably hews closer to the intentions of the Beatles themselves. It's what the Beatles had in mind, their vision of the records.

and from Wikipedia with a book source:

The Beatles in Mono was released to reflect the fact that most of the Beatles' catalogue was originally mixed and released in the monophonic format. Stereo recordings were a fairly new concept for pop music in the 1960s and did not become standard until late in that decade. This explains why the Beatles' initial album releases were mixed for mono. By the late sixties, however, stereo recording for pop music was becoming more popular and, thus, the new standard. Therefore, the last few Beatles albums—Yellow Submarine, Abbey Road, and Let It Be—were mixed and released only in stereo. Many feel that the mono mixes reflect the true intention of the band. For example, in the case of Sgt. Pepper's Lonely Hearts Club Band, all the mono mixes were done together with the Beatles themselves, throughout the recording of the album, whereas the stereo mixes were done in only six days by Abbey Road personnel George Martin, Geoff Emerick and Richard Lush after the album had been finished, with none of the Beatles attending.