I don't think the situation with Cloud's mind is so clear cut. I mean, his subconscious and conscious minds appear to have been separate personalities, considering they interacted to some extent. But at the same time, Cloud also had moments that were genuinely him. While Zack had an effect, on the way he acted, it doesn't seem to be as prominent as many seem to believe, with other elements that don't fit with Zack's established personality. However, I think a lot of that stemmed more from dissociation than mind control. I got the impression that stuff like that only really came into play in the obvious moments like at the temple of the ancients, with the rest being more standard psychological manipulation where people are tricked into doing what someone wants without having their thoughts controlled on a supernatural level.
While Cloud had a lot of issues, he was still sufficiently himself to resist Sephiroth's attempts at controlling him to some extent even when Sephiroth managed to get him to do stuff like hand over the black materia. And then it wasn't really a problem when he figured out who he really was. From what I gather, Sephiroth had to catch him off-guard and use regular manipulation methods to make him vulnerable to that.
Basically, even with the whole memory copying thing, I think Cloud's issues are the result of a more mundane take on psychological issues than a literal patchwork of his personality, Zack's personality and Jenova/Sephiroth's will. Rather, regardless of the exact details of Cloud ending up with bits of Zack and Tifa's memories, it was his mind's attempt at coping with trauma by distancing itself from it that led to Cloud adopting a different personality rather than Sephiroth engineering it for ease of manipulation. Rather, he saw an opportunity and exploited it mercilessly to get back at Cloud for killing him, which is something he never really got over.
For how that would effect dialogue, I figure Cloud's false persona has some consistency to it, but also adapts to the situation, like how the cockiness was mostly dropped somewhere between meeting Aerith and leaving Midgar. Rather than label options the way that was suggested, it'd be better to have the possible responses not be constrained by those, while still giving options like a nice response, an indifferent response and so on depending on the situation. I mean if it's situation where only various ways to tell the person to go screw themselves makes sense, it's not like much more than the wording will be different, though one will likely be more humorous in some way.