Ubi bought the M7M assets from 3BO almost exclusively for the rights to the HoMM series. They cared very, very little about the RPG franchise. We RPG fans are essentially orphaned.
They released their own version of MM9 with very few changes. Those changes included 1) a modified title page, 2) a more restrictive EULA, and 3) an *earlier* version of the game engine that NWC had developed.
Nothing in the Ubi files that I'm aware of identifies itself as version 1.3, nor has Ubi ever released a patch for MM9. I suspect that this 1.3 designation at Gamestop was applied by someone who either guessed badly or is underinformed.