I mean, the idea of some sort of collective consciousness between Jenova recipients is kind of a core plot point of the game
Sephiroth/Jenova exerting control over people with the cells in them happens yes - extracting memories from one person and feeding it to another? There's nothing in the original to suggest that is happening.
- that's how Reunion works,
Reunion is simply a calling between the cells. It's never said to be some kind of conscious process from the main cluster that would indicate it could rummage through people's memories, extract the pertinent ones for some grand plot and then feed them to Cloud.
It doesn't even make sense.
Why would Jenova enforce Cloud's delusion? What possible reason, at that point in the plot, would Jenova have to reshape Cloud's personality?
To accept that explanation of events, Jenova would have to be A.) capable of rummaging through Zack's memories after he is already dead, and then plant them in Cloud's head, and B.) she/it would have to have a reason to do that despite the fact that this conflicts with the narrative indicating that Jenova awakens in Shinra building when Cloud comes there (after all, if she was already awake, doing stuff like manipulating Cloud, why didn't she break out earlier?)
In the original, Cloud's mind is being messed with by Sephiroth's conscious efforts through the Jenova cells.
Since Sephiroth didn't have Cloud on his radar back when Cloud woke up in Midgar after Zack died, he wouldn't have done it either.
and how Sephiroth manages to appear to the player several times without ever leaving the crater
That's not at all how Sephiroth appears outside of the crater. The Sephiroth you encounter outside the crater is the Jenova that broke out of Shinra building taking on Sephiroth's form.
- he's imprinting himself on Jenova-infused people, the 'Sephiroth clones' (God, clone was such a poor choice of words in the original translation). That's in the Ultimania.
Where in the Ultimania is that? Even if it was though, the problem is that the Ultimania guide was released September 9, 2005.
Whatever in that guide has no bearing on whether or not something was thought up when the game was first made and released, and has no bearing on this discussion since this is a discussion on what was intended with the original not about what has been made the case post hoc through compilation ret-cons, which it is likely to contain given it was released only days before Advent Children, likely as a part of the FFVII compilation initiative.