I think if you get the Mono box, then all you need are the Abbey Road and Let It Be stereo cds, and you'll have all of their official "canon" studio recordings. Except for Yellow Submarine, but as mentioned the remaining Beatles tracks from YS are on the Mono Masters set anyway. The rest of YS is George Martin's orchestral music that the Beatles don't perform on.
If you want a "complete" collection, you might want to pick up the two Capitol Album box sets (i.e. the U.S. editions), the Yellow Submarine Songtrack (different than the above Yellow Submarine), Love, Let it Be Naked, the Live at the BBC set, and the 3 Anthology releases. Plus maybe the Hamburg studio recordings (out on numerous releases in different configurations), though that predates their first official Beatles release. I think that's it.
At least I think that would be complete as far as CD releases - there are also things that haven't been released on CD, like the Hollywood Bowl live album.