A quick run-down of my theory is... This is an "unknown" journey, but only because where we stand right now, we "think" they're going to veer off course. I personally think it's a fake out unless confirmed otherwise by Square. Or at the very least... There's more to it than what we're aware of (obviously).
Something interesting to note is that the Whispers in the beginning were bothering Aerith, and it's only because Cloud touched her is when we and he can also see these things as well. Now, theses "whispers" are supposed to be the Watchmen of Fate, in order to make sure nothing deviates off the course of the original canon. They only interfere when someone is about to do something that defies the destiny revolving around the Planet. So then why bother Aerith? Because Aerith also planned to change fate from the very beginning -- she's also "unnatural", clearly she knows too much by what the last chapter shows.
Isn't it strange that when the Sector 7 Plate was about to fall, and she went to save Marlene, we saw a "glitch" like what happens with Cloud and his memories? Right after that, Marlene stops crying and backs away like she wants to say something, but then Aerith shushes her, implying whatever Marlene saw is a big secret. The next time Marlene mentions Aerith to Barret, she says "She's kinda..." and hesitates. She's not supposed to say what she saw. And then she says, "You should help her." This exact phenomenon occurs when Aerith puts her hand on Red XIII's head. After that, he had knowledge of what the Whispers were. It's been made abundantly clear, but she's equally as "foreign" as Sephiroth seems to be. But, Sephiroth's goals and Aerith's goals are different from each other. However, both of them know things they "canonically" shouldn't. This might be why Aerith gives Cloud the flower that symbolizes "Reunion", even though they're meeting for the first time. If you're an OG fan, we're made to think "She's seeing Zack in Cloud" and that's true too, but I think there's more to it.
The game has touched on it numerous times that the Whispers are invisible unless you've made contact with someone who can see them. Remember the morning after the mission with Jessie? You're fighting the Whispers and you don't see anybody else around but the main party + Avalanche, but you know what the people in the S7 Slums say? "What was all the commotion about?" "What were they shooting at? It looked like they were shooting at nothing." As well, remember when Cloud first meets Aerith, and only the two of them can see the Whispers? But the Shinra Public Security Infantrymen can't? Only we see these entities.
But think about it. Right after everything that happens, the goal remains the same -- to stop Sephiroth. The only ones truly privy to the information that happened previously would be Sephiroth, Aertith, Red XIII and possibly Marlene (but she's a kid lmao, so she's a non-factor). Red is claiming that the events that what happened in the OG is the failed timeline, but it's never stated exactly what's the defining moment that determines this. Sephiroth asked Cloud to join him and defy destiny, but Cloud refuses. A similar showdown happens, like in the original when Cloud used Omnislash, only this time Cloud loses because he's nowhere near strong enough. That's when he says, "Not quite." (Or something along those lines). Then he says, "Seven seconds until the end." (Going off the Chapter description, he's referring to the Planet.) My interpretation of this is that Cloud isn't yet capable of bringing about the change Sephiroth wants, so for now, he most likely won't be interfering.
What about all of this does it actually change? Nothing, at least for most of Part 2 I'd wager. The only time you're gonna most likely see any changes would be in Aerith's motivations and decisions, and just like in the OG, she's probably not going to tell anyone (especially Cloud) what lies ahead and what her plans are. Let's also not forget that at this point in time in the OG, this isn't actually Sephiroth we're dealing with, but Jenova through Sephiroth's will. And something to note, is that the Jenova form you fight in Ch.17 is called "Dreamweaver"... Which is known to cause hallucinations (stated in the Asses Menu and by Red XIII). It's possible that a lot of what "Sephiroth" (Jenova) is showing Cloud are "images" and "memories". Even so, that still doesn't detract the party's main goal and that has been affirmed at the end. Saving the Planet, stopping Sephiroth, all of that is still the same.
As for Zack, it's possible that what we ended up seeing isn't actually a tangible timeline that we're now in, but moreso showing a "possibility of what could've been". I'm still shaky on this part, so I'll have to dwell on it more, but I don't think Zack is alive. If he is, my offhand guess is for any AU purposes Square decides to do later on.
I get he wanted to see Aerith, but still. Cloud is one thing because even in the Remake, they make it a point for the regular Shinra staff to be like "Who is this guy?" so it's perfectly reasonable for him to fly under the radar. The game also makes it clear that the Infantrymen are expendable and none of the top brass bother to even learn their names. 
Then when they go back to Midgar finally, it's like in the original only instead of Midgar's Avalanche being the one and only group, now it's a bigger mission including Barret, Biggs, Jessie and Wedge. Zack is the one you play as, but you start seeing Cloud grow more and more because Zack is helping Cloud out of his depression due to not being able to protect his loved ones like his family and Tifa. Almost in a kind of Kamina and Simon sort of bond. Idunno, there's a lot of places they could've taken a "Zack is alive FF7" story. I still think it'd come down to Cloud vs. Sephiroth because Cloud's the one who ended up knocking the guy off. Cloud in this version would essentially be Gohan's journey leading up to when he finally goes Super Saiyan 2. Whether it'd be compelling though, or even good though... Depends on the writer.