yes and no.
It's the same ending, just at 100% you get the "extended" cut.
or rather, at 12/14 Most wanted you get a cut down version of the ending that doesn't offer proper closure
This game has 1 real ending, basically, and that's at 100%
* Finishing the main storyline is nice and changes a few lines of dialogue within the game, but it doesn't end the Arkham trilogy.
* Finishing 12 of 14 most wanted will tease you by showing you individual parts of the actual ending and literally tell you "finish all of the most wanted quests to reveal the true ending"
* Finishing 14 of 14 serves as the one, true, canonical, ending.