The sad thing is, Sony or EA is not confirming if cross buy really exists... shame on Sony!
However, I have stated with an alternate post that the PS3 version states in the purchase agreement that in includes licenses for 2 consoles and 2 portable units.
Now to answer your question… The $59.99 list price is common for most PS3 games and $39.99 is the common list price for Vita games. However when referring to the cross buy program, the common list price appears to be $59.99 which includes both PS3 and Vita platforms (at least this is the pricing for Playstation All-stars ~ $59.99 PS3 and Vita versus $39.99 for Vita only). You see, it wouldn’t be fair to charge everyone $59.99 as not all Vita users have a PS3. Therefore, $39.99 is a good price point for the Vita only version, while $59.99 is a generous price model for games which support the cross-buy program.
Marketing management should be smart enough to realize that the common consumer will not pay $100 to play NFS:MW on both the Vita and PS3 when it’s basically the same game on both systems (only minor differences between the two systems).
Now Assassins Creed 3 and Assassins Creed 3 Liberation are two different games for each platform. Some consumers may pay $100 for both games, however I think I will choose one platform over the other. I believe I will probably buy Liberation for the Vita as AC games get cheap really fast with the re-sale market. I expect the Vita version to sustain its used value much longer.