Loving that lots of confusion within the original timeline and obviously problematic questions are being tackled in this game such as:
"Why would the Lifestream create a materia that can destroy itself?"
It didn't. There was a particularly powerful materia that the Gi essentially Sauron'd into the Black Materia.
"How could regular bullets kills Zack if FF7 characters are so strong?"
They aren't regular at all. The weapons created by Shinra are made of magical metal alloys and enhanced by materia.
"What happened to the Cetra? Why did they die off if they were so strong?"
Humanity, most likely influenced by Jenova, turned on the Cetra and hunted them down after they were already greatly diminished by their initial conflict with alien shapeshifter. In OG, it was implied that Jenova nearly killed all of the Cetra.
Although it is suggested by the Gi that the Cetra were selfish, jealous, ignorant, and liars, they were 100% correct in thinking that the things that cannot join the Lifestream seem to be the biggest threat to existence. The creation of the Black Materia (Gi couldn't die and got pissed enough to try and do something about it), Jenova (couldn't truly die and just hibernated until Shinra discovered her, creating...), Sephiroth (fucker refuses to be diffused into the Lifestream and comes back to cause all of this), etc.
Sephiroth actively says that he is going to take over infinity. His next statement directly confirms that he means all the new universes created by unbound fate and unwritten stories. It seems that he is implying that he will do this by merging all timelines.
"My fragmented mother, these errant worlds... All shall be one again."
Now for some other stuff:
We see that Sephiroth (& another version of Aerith - OG/Advent Children version most likely) has the ability to travel between these universes/timelines freely, can send people between universes/timelines easily (does it to Zack twice, separates Cloud from the party, etc), but is the only one shown that doesn't seem to have multiple versions of himself existing (might be like a shared consciousness type of thing or if not then like dreamwalking in the MCU where he can take over a version of himself that already exists in that timeline).
Cloud seems to be some type of nexus point for these alternate worlds. Zack could perceive Cloud in another timeline and when Zack touches him it brings them into the same universe together. Cloud is able to take the white materia from another universe and bring it into the Rebirth timeline. He can see Aerith when no one else can.
There are two reunions. The OG explanation of Jenova's shit coming back together AND the coalescing of timelines. While that is happening, Sephiroth seems to have a specific goal in mind that pertains to his true self in-between worlds. The Black Materia is the focal point for this. He seemed to have orchestrated/set his sights on a timeline where the White Materia was neutralized and then didn't seem happy when Cloud brought another one into play. OG/AC Aerith is actively working against him through multiple timelines.
For interesting power-scaling purposes, we see that Sephiroth sends a Bizarro version of himself against everyone through multiple timelines. When it is defeated by Cloud solo, it moves into the timeline with the rest of the party present. When it is defeated there, it moves over to deal with Zack (aided by Aerith) in another timeline.
Cloud >= Zack (aided by Aerith) >= Rest of the Party > Bizarro Sephiroth.
Also, Cloud and OG/AC Aerith are able to pressure and put AC Sephiroth on the backfoot. It actually shows him going down to one knee before he flies off and then laughs.
I think the main difference in AC Sephiroth's motivation this time around is that he going to actively use the Black Materia to destroy the Lifestream and not just to injure the planet and try to absorb the spirit energy. He actively states that this was this desire in Advent Children. He probably realized that fucking around with half-measures isn't going to work. He has a near-equal in the timeline with Aerith. The Lifestream is defending itself with all of its resources. And Cloud & Company are actively trying to fuck his shit up at the same time. Now throw in Zack as another agent working to ensure his demise.