Rumors have it that the cover to Yesterday...and Today was originally intended chosen as the famous "butcher shot." However, after considerable negative feedback, Capitol hastily replaced the photo with a random shot that they had lying around. That cover, designed from scratch in five days, became the replacement "trunk" cover. I have never believed that theory.
In the early 1980's, I developed a theory that while, yes, the final design for the "trunk cover" was hastily put together, the existing mock-ups showed that the trunk cover was around at the same time as the "butcher" cover and may have been the original design for the cover. For a short time recently, I abandoned that theory, but thanks to the research of Bruce Spizer, I am now thoroughly convinced that the "trunk is original" hypothesis is correct. For those who require proof, purchase Bruce's book, "The Beatles' Story on Capitol Records, Part Two," which is now available.
Given Bruce's essential reasoning and proof, here is what I have believed to be the order of composition of the Yesterday...and Today covers:

Those alternate slicks that have emerged show that the Y & T cover was not always intended to be a "paste-over." Nor was it intended to be a butcher cover. Shortly before the album was compiled, but after May 10, 1966 when the three Revolver songs were chosen and mixed into mono for the US album, designs using the "trunk" photo were mocked up. This particular design puts the "trunk" photo at the right and fills the rest of the cover with writing. This was the original design, with the whole title in quotation marks. No slicks exist of the cover in this form; instead, an four color separation provides the only surviving indication that this cover had been designed.

The mistake in putting the quotation marks around the whole title -- instead of just around the "Yesterday" song title -- was quickly corrected. Had the LP been released then, it likely would have come out in this form. In addition to the four color separations, slicks were prepared of this modified design as it was being prepared for release.

This other altenate trunk cover was more creative in certain respects. The group's name appears above the photo, which is tilted. The white part of the cover seems to detract from the simple beauty of the first version, however. Slicks were also prepared of this form.
These trunk cover mock-ups were made prior to the creation of the butcher cover. The Beatles were particularly keen on the new photo, though. The butcher photograph was supposed to demystify the Beatles. Ironically, though, John Lennon's comment that the Beatles were more popular than Jesus, taken out of context and circulated as the Beatles were touring (that same year) had much of the effect that the picture was supposed to have.
The butcher cover to the North American Yesterday...and Today album was a piece of "pop art satire." Also used to promote the "Paperback Writer" single in England, the cover was seen as little more than a bit of surrealism by the Beatles themselves. If you read the article at Saki's site about the "butcher cover," you know that in the form it was released, it is an unfinished piece. Intended to be gilted in gold, the photograph (called, properly, "A Somnambulant Adventure") was part of a group of three photos that were intended to debunk the Beatles' legendary status. The mental image was supposed to form that these guys were just humans after all. John (and later Paul) have said that it was a commentary on war.
But the completed idea was not to see the light of day. Instead,
the uncropped final "butcher" photo was sent to Ted Staidle, a professional
photographer in the United States whose company -- Staidle and
Associates -- prepared photographic proofs for Capitol Records during
the 1960's. He created exactly two copies of the 16" by 20" proof -- one for
Capitol and one for his files. Capitol's copy of the Staidle proof
was kept by the record company and eventually surfaced as the inside
front cover to the Rarities album in 1980. Staidle's copy
was kept by his offices for 35 years and sold at private auction.

When Capitol's art department approved of the proofs, they selected the paper stock and chose the color scheme for the stereo banner (at the top of the stereo LP) and the font and color of the song titles. Originally, the album design was to feature quotes around "Yesterday," which you also note are in the mock-ups above. These were removed, though, since apparently they were thought to detract from the design. Like the early trunk cover designs, considerable thought went into the butcher cover.
Here's a slick without the Capitol logo, thought to have been prepared so that the logo would be sized and placed properly.

A copy of the above slick with the logo pasted on by hand with notes as to its placement has also surfaced. It is surely the only such copy. Once all of the type was in place, the cover was ready for release.

As the radio stations got their copies, it seemed like every one of them was grumbling about THAT cover. [John Lennon and Yoko Ono would cause a similar stir two years later with Two Virgins.] So, before the official release date, Capitol issued a letter recalling the album. Pulling out another photograph of the Beatles by the same photographer (and reversing it), Capitol went to work fashioning a replacement cover for the album, using the photograph from the trunk cover design.

In order to quickly replace the butcher cover, the background of the replacement photo was airbrushed white, and the printing from the "butcher" version was laid on top of the new graphics. Alternate forms do exist, but these lack the artistic flair that went into creating the earlier "trunk" designs. Although the order had been given to destroy the old covers, it was more cost- and time-efficient to glue the new front cover on top of the rejected "butcher" covers. Doing this saved time, and the new records were on the stands within five days. This is an amazing turn-around time, considering the fact that the mono pasteover is not exactly rare. It appears, though, that the Jacksonville, IL, plant did destroy nearly all of their butchers.
Tape copies of the Yesterday...and Today LP also featured the trunk cover, and since they were prepared after the recall of the butcher covers, no tape copies exist with the butcher cover design. It appears that some thought was given, though, to rethinking the bland, whitewashed cover. When the eight track of Yesterday...and Today was issued by itself in 1968 (apart from Beatles VI), some color was added to its cover. However, since by that time the album was no longer an important seller, the decision was made to scrap the idea of putting a more artistic cover on Yesterday...and Today. Instead, a "Gold Record Award" was added to the existing "white" trunk cover, and the other cover designs were never used. The later cassette issue of the album also features the usual airbrushed cover.
Yesterday and Today Covers