The Dragon Quest problem is an issue with the composer. By my understanding, Koichi Sugiyama owns the rights to the music in Dragon Quest (he even gets a special copyright section in Hero's Smash reveal trailer), and while I can't find a specific source on this, it seems as though he only allows Square-Enix to use the Midi versions of songs so that, if people want to hear the orchestral versions, they have to go to his concerts, where he gets a bigger cut of the profits.
No idea why Life Will Change, Opening/Bombing Mission, and the Chocobo theme aren't in Smash, though, since they were in Joker's trailer, Cloud's trailer, and the Chocobo Mii hat trailer, respectively. (maybe the Chocobo theme didn't fit Midgar, but the other two seem unjustified)