Final Fantasy VII Remake based its entire story around the concept of the series not using the same story as Final Fantasy VII. The members of Avalanche managed to defy their fate, which means that future entries are not tied to pre-destined events. Aerith no longer has to die, the Weapon monsters might not be unleashed on the world, and Sephiroth could succeed in his plans.
It's clear that the world of Final Fantasy VII Remake is not the same as that of Final Fantasy VII. The fact that the original version of Avalanche from Before Crisis is still active means that there has already been some divergence in the timeline. The answer as to what caused these changes might have been revealed a long time ago and in a whole other Final Fantasy game, as it's possible that Final Fantasy VII Remake happened as a result of Final Fantasy Tactics.
The Zack Scene & Multiple Timelines
There is a moment near the end of Final Fantasy VII Remake where the player is given a glimpse of Zack's last stand from Crisis Core. We are then shown an alternate version of events, where Zack defeated the Shinra army and he made it to Midgar with Cloud. Aerith and Zack seemingly glimpse each other as they pass. This scene cements the idea that there are multiple timelines happening in the Final Fantasy VII Remake and it's established that Red XIII's "500 Years Later" scene from Final Fantasy VII might not come to pass.
Cloud Never Left Ivalice
It's clear that Sephiroth knows more than he's letting on and the fact that he revealed himself so early in the Final Fantasy VII Remake world means that he's trying to influence events going forward. It's possible that the version of Sephiroth we see in Final Fantasy VII Remake comes from an alternate timeline, one that may have been hinted at all the way back in '97.
Final Fantasy Tactics was a tactical RPG that was released for the original PlayStation. It was set in the world of Ivalice, which later acted as the setting for Final Fantasy XII. It was possible for the player to unlock Cloud as a playable character in Final Fantasy Tactics through the means of a device that called him from another dimension. It's suggested that Cloud is pulled from his own world at the same point as when he first fell into the Lifestream in Final Fantasy VII, which is why his memories are still hazy when he arrives in Ivalice.
Cloud's story is never resolved in Final Fantasy Tactics. Once he joins the party, he has no significant role in the story of the game. Cloud is still with the party at the end of Final Fantasy Tactics and it's never established how he returned to his own world.
There could exist a timeline where Cloud never returned from Ivalice and a fractured Avalanche was unable to stop Sephiroth's plans. Meteor hit the planet and Sephiroth absorbed the power of the Lifestream, becoming a god.
Sephiroth Isn't A Threat To Time - He's A Threat To The Multiverse
The Final Fantasy series exists in a connected multiverse. It has been established that Gilgamesh from Final Fantasy V is traveling the universe while searching for a way home. The Dissidia series has crossed over characters from all of the Final Fantasy games on several occasions. This raises the question of why the Whispers have appeared in the world of Final Fantasy VII Remake to try and make sure that fate takes its course, but these other crossovers can happen unabated?
If Sephiroth succeeded in a timeline without a Cloud to oppose him and achieved ultimate power, then he could have gained the ability to influence time itself. The reason why the Whispers are trying to make sure that the events of Final Fantasy VII happen is that Sephiroth is trying to change time itself in his homeworld as part of a bid to gain more power. In Final Fantasy VII Remake, Sephiroth brings Cloud to a strange dimension that appears to be in outer space, which he refers to as the "edge of creation". Sephiroth's goal could have moved on from godhood and he has become a threat to creation itself. This raises the stakes for future entries in the Final Fantasy VII Remake series, as the entire cosmos is at risk, while Sephiroth is stronger than he was before. The entire story could be linked to a single loose end from Final Fantasy Tactics and a Cloud that never managed to make his way home.
Final Fantasy VII Remake is available now on PlayStation 4.