There's no reason to believe it works the same way with every person. If you compare the way Lien performs when Tieran is clearly in control to the way she performs in the early scenes, there is a marked difference. To me, that was the period of transition.
Additionally, what purpose does it serve to "get Neelix out of the way?" Surely breaking up with him would only encourage him to keep bothering her and want to discuss things. Wouldn't it be far more in Tieran's interests to maintain the status quo before escaping?
Plus let's not forget that there is a scene in the transporter room where Kes explains the transporters to Adin which takes place "after" she has been infected with Tieran. She is alone with him so why would Tieran maintain the charade with his personal physician?
I definitely think a case can be made for Kes essentially still being in control during the break-up.
Well, I don't think there's any reason even hinted at, that suggests that it works any differently with any individual of any species. That's mere supposition. The Doctor later details the transfer process and neither he nor Tuvok, who
did have confidence in Kes's ability and will to resist, suggested that her physiology or psionic abilities would have prevented her from being immediately inhabited. Neither did Janeway, who was insistent only that it had to be established that Kes's personality couldn't be restored, which soon became doable with the Doctor's doohickey. Demmas's assertions in the matter can be discounted as he doesn't even know how Tieran came to be able to achieve this ability.
What you see as a period of transition, marked by differences in Kes's affect can much more plausibly explained, I believe, by the simple application of subterfuge that Tieran would naturally adopt until he felt secure to freely express himself once off the ship. There would be no sense in him blatantly revealing anything of himself when such a drastic difference in Kes's behavior would be hard to conceal from any number of people, perhaps Tuvok most critically. I think in fact that it may have been his design to further emphasize Kes's empathic nature, by spending so much time with Nori in a situation that would seem to justify that investment as a means to have the opportunity to set the plans for escape in motion.
The point you make about the scene in the transporter room made me wonder about the perspective of the shot and try to recall what we actually see. I took a look at it and indeed the transporter officer is clearly visible at his station, so while Tieran can give a generic introduction of the set-up to Nori and Adin, he is obviously not at liberty to speak to them freely. Also, as a point to suggest that supports the idea that this shows Tieran wholly in control before the break-up with Neelix, what would be the purpose of Kes giving a tour of the transporter room at all, if not as a clear foreshadowing of the events to come?
As to the situation with Neelix and the need for Tieran to do anything as drastic as changing their dynamic, I think a few reasons can be applied without too much elaboration or the need to question the effort. First, and most simply, it was most convenient for Tieran not to have any unnecessary claims on his time as he not only prepared the escape but also had to make sure that Nori and Adin were also prepped and ready to accomplish their roles in the plan. Going past that rationale, I believe we're led to a much more interesting part of the equation as regards both Tieran and Kes. Tieran is innately very perceptive and combined with, what I believe, is the sense that he's already utilizing Kes's abilities, most likely with less constraint than we see planet side when she is more and more effective on breaking him down, he's almost certainly aware of the history of the relationship and the depth of Neelix's feeling for Kes. So aside from Neelix merely being a distraction, Tieran can reasonably be concerned that even in the brief time left before his party leaves Voyager, Neelix might intuit a difference, something perhaps imperceptible to anyone else, in how Kes seems to be acting, that isn't true to her, that could be a potential danger to the smooth execution of what is imminently to take place. I think that here one should keep in mind that Tieran is nothing if not a thorough and rigorous planner and tactician.
What I've long found compelling, if subtle perhaps, is what imparts a truly personal aspect to all three characters involved in the break-up. The devastating impact on Neelix of something he would never have anticipated, but is made convincing by Tieran's artful construction of why it has to take place, goes without saying. The involvement of Tieran himself, and most surprisingly, Kes, is what makes the scene captivating. We're not meant to give Tieran any consideration than as a paranoid, devious despot whose refusal as a consciousness to give up the pursuit of the power that he believes is rightfully his, will brook no compromise or surrender.
But here, I believe we see a sense of regret in doing what he knows is required. Why regret? Because he knows what is about to happen will prove to be irrevocable and even he's not insensitive to what it will mean. However, that he knows this breach is justified, aside from his own considerations, is where Kes herself comes into play. Tieran knows her mind and feelings intimately and what is clear to him is that she has come to a point in her knowledge of herself and how her needs have evolved, that even if perhaps below the level of her own consciousness, this change in her life and circumstances is what she has come to recognize as a decision that is of her own accord. So there is an actual symbiosis of sorts going on, even with Kes being so deeply submerged at this time. I think it's a tribute to Jennifer Lien's skills that this encounter is rendered not as a expediency roughly and unfeelingly carried out, but as a sad and touching elegy to a committed relationship that for both Neelix and Kes had been an unreserved and unquestionable defining truth. That Tieran himself is moved, I think is indicated by the grace note of Lien's regretful and sorrowful slight turn of her head as she gets up to leave the table and Neelix in the sense that they had always know each other, forever.
This interpretation is just that, but one that I feel is substantiated by what we're explicitly informed about the transfer that gives no reason to believe that it didn't fully take place as explained, and the behavior of who I believe, is Tieran all along, that supports the action to come rather than plausibly is the normal behavior of Kes as we know her. Finally, I just don't think that she would have taken the momentous step of breaking up with Neelix so decisively, at this time or in this manner herself, as again, while the knowledge may have been inside her, there was nothing that we had seen in previous episodes that would suggest that this would be a logical time for an observed progression of an awareness, that had
not been witnessed before, was suddenly ready for fruition. Of course Voyager has been pointed to more than a few times for inconsistencies or plain ignoring of continuity. I just don't think this represents such an example.
You also earlier remarked that the relationship's end is confirmed in Darkling. As Ethan Phillips has mentioned frequently in convention appearances, the reality of what absolutely and finally occurred in Warlord, was acknowledged in a scene in Fair Trade, in which the two admit what has happened, while saying that they remain as friends who care about each other. The fact that the scene didn't make the final cut, might define it as something that never happened to strict canon constructionists, but my perspective is that the writer wrote it, it was performed, and its intention was not mitigated by a decision determined solely by time constraints.