I haven't read this whole thread so I don't know if my opinion has been stated before, but even if it has this post still has merit because it includes my list.
I think that although The Beatles didn't specifically choose the track listing of Magical Mystery Tour, they clearly approved of it, because they could have easily placed the double EP and singles onto Past Masters like they did with all the other EPs and singles when making the CDs, but they didn't. Also, they didn't choose the track lists themselves for their early British albums either; as far as I'm aware, George Martin did that, and the Beatles main input was just approval, much like Magical Mystery Tour. The Beatles didn't care about the artistic integrity of the album as a whole in the early days. They only cared, in a loose way, about how it flowed. In fact, once the band broke up, they almost completely stopped making single-unit "art" records and considered them mostly as collections of individual tracks. Therefore, I think Magical Mystery Tour counts as a Beatles album worthy of serious discussion. And it's one of my favorites, to boot.
Here's my list of their canon albums, not including Love and Yellow Submarine Songtrack, which are just remixes and not original material, and Past Masters, which is merely a strictly chronological collection of singles and miscellanea and not ordered to be listened to as an album in its own right, unlike Magical Mystery Tour which was ordered in a coherent way:
1. Revolver
2. Magical Mystery Tour
3. Rubber Soul
4. Sgt. Pepper's Lonely Hearts Club Band
5. The Beatles
6. Beatles For Sale
7. Please Please Me
8. Let It Be ...Naked
9. Let It Be
10. Yellow Submarine
11. Help!
12. A Hard Day's Night
13. With The Beatles