"All quests" in Final Fantasy 7 Rebirth have 2 versions because the devs wanted to include a story detail from the original JRPG

gamesradar.com:

Final Fantasy 7 Rebirth has two versions of each quest due to Square Enix's desire to include a story detail from the original JRPG.

Taking advantage of modern technology, Final Fantasy 7 Rebirth will feature a much more open and expansive world than the original Final Fantasy 7. As such, players might encounter quests in a different order from how they did in the PS1 game. This posed a problem for the developer when it came to incorporating one plot point in particular from the iconic JRPG.

Warning: the below contains spoilers for the original Final Fantasy 7, so if you've not played the PS1 classic, you might want to avert your gaze.

During their journey, Cloud and his companions visit Cosmo Canyon, the birthplace of Red XIII.  Here, it's revealed that Red XIII's real name is Nanaki, and through the events that transpire, he learns the truth about his father, who, until now, he believed to be a coward who abandoned his tribe. His mindset changes as a result, and so too does his dialogue.

Because of this, the developer has included two different versions of the game's quests, one for players who have witnessed his transformation at Cosmo Canyon and one for those who haven't.

This was revealed by Final Fantasy 7 Rebirth director Naoki Hamaguchi in a recent interview with Screen Rant. "A fun little tidbit that I wanted to share about that is in the original, you may remember that Red XIII, if you go to Cosmo Canyon, once you go there, his personality changes a bit," he explains. 

"And considering that his personality changes, we have it designed so that all quests in the game kind of have a Red XIII and a Nanaki version. So for people, it has all options available for that."

This suggests that the events in Cosmo Canyon