The current CDs have been on the market now for 20 years, and have various problems. When issued on vinyl, the majority of the albums were avaialble in both stereo and mono versions, yet the CDs contain either the original mono mix, the original stereo mix or a 1987 remix. The singles tracks on the Past Masters compilations are often in stereo despite the original UK versions being in mono, but mono mixes did appear on the singles box set. It's even more complicated when you get to Magical Mystery Tour, which was not issued in LP form in the UK until 1976, and I wont enter into that here. There's also a few other mixes that appeared over the years on non-UK pressings and/or promo singles that have also not appeared on CD.
The catalogue was re-mastered some time ago, I gather, as I'm in contact with someone who managed to see pre-release internal EMI copies of some of the remastered albums before a previous release was cancelled. Apparently these contained both stereo and mono versions where applicable. Aside from some missing mixes, there's also the Live At The Hollywood Bowl album and fan club flexidiscs to take care of, as well as perhaps a few out-takes that did make the Anthology project.
As for the Michael Jackson issue, he acquired ATV music in the early 1980s. ATV had in in turn acquired Northern Songs, the Beatles publishing company, many years previous. Northern Songs owned the publishing rights to most of their own compositions. The exceptions being later George Harrison compositions, Ringo's two compositions, and both sides of the first two UK singles which were issued initially before Northern Songs was formed.