The Criterion Collection released The Life Aquatic with Steve Zissou on blu-ray back in May, the first appearance of the film on that format. The source for this disc was a "new, restored 4K film transfer, supervised by director Wes Anderson." However, long before this release, the film had been available for rental and purchase in 1080p HD by the Vudu service. Having seen both versions, it's very clear that these are different masters. The Vudu version, for example, appears to be much sharper, while the Criterion boasts a more "filmic" transfer. Did the Vudu version not come from a 4K film transfer? How many different HD masters of films are floating around out there?
A distribution network will typically hold on to their prints for as long as possible (I.E they hold the rights to it): in the era of digital distribution that extends to exhibition itself, this is becoming easier and easier.
Increasingly, edits are drawn from the original, 4K exhibition quality 'Copy' and are subjected to certain cuts. Sometimes, this process is reversed to the benefit of the Post-release market (Content that had to be removed to obtain a rating that would have produced a stricter classification; think "_ _ _ :Uncut"
Quality of transfer is not the only criteria that substantiates the release of different versions.
Typically, a higher quality approximate of an exibition quality will arrive when there is a market for it: until then, the 'version' doesn't exist outside the archives of the exhibition company responsible for its distribution...