Perhaps it wouldn't destroy those early developments, but it would unnecessarily cheapen a plethora of important decisions and significant character development from early Genshiken, and it's just not worth it at this point in the story, since it would ultimately occur solely in order to satisfy a small, but vocal, section of readers who have continuously hoped that Saki would somehow discard her feelings for Kousaka at some point, so that she can miraculously end up with Madarame, a person she's never had any romantic feelings for. Yes, people do often break up, but it's much more rare for people to fall out of love, which is what would be required here.
I've always thought Saki and Kousaka are an excellent couple, with pretty great chemistry, and, at the very least, they have far more realistic and believable chemistry than any she would have with Madarame were they to become a couple. Yes, their chemistry is quite good in Spotted Flower, but I really don't think it would translate well here at all.
A Spotted Flower end has always been an extremely slim possibility to me, and it remains so, due to the noticeable lack of proper and realistic foreshadowing to this eventual outcome. I do believe Kio wants to keep us guessing about the actual nature of Spotted Flower, but I also greatly believe it's an alternate universe, due to the rather strong likelihood that he wouldn't want to reveal their names or connections simply because of the very real possibility that it would prematurely cause many more readers to suddenly consider that as the true end of Genshiken. I also just think it was written to satisfy and appeal to a portion of readers (the Saki and Madarame shippers) that might otherwise not be satisfied by the actual conclusion of Genshiken.
Spoiler:
Yet, I have to look at Madarame's intentions behind the question he asked Saki, because it effectively undercuts his admirable decision to refrain from disturbing the Saki and Kousaka relationship with his own selfish hopes for his love of Saki to be returned. Basically, I just think, as always, that Kio's simply teasing the shippers of this particular pairing, without ever showing any actual evidence that would support it ever coming to fruition. At this point, I'd honestly want him to end up with anyone from his small harem rather than Saki, which I now think is an even more likely direction for Kio to take, due to the distinct possibility that Madarame will finally move on following this rejection. However vaguely worded said rejection might have seemed, it was still a rejection.
Still, despite all this analysis, the biggest part necessary for this eventual outcome is Saki breaking it off and falling out of love with Kousaka, which I don't see happening at all, without these moments coming off as unsatisfying, unnecessary and completely contrived, since there's been no hints toward any legitimate reasoning as to why she would ever do this. Also, I just don't think Kio would dissolve a relationship that satisfyingly developed throughout the entirety of early Genshiken, unless he wants to turn off a considerable section of the fanbase from continuing to read this.
In the end, however strongly I disagree with some of your points, I do somewhat understand your reasoning as to the possibility of this turning into a Spotted Flower conclusion, but do you honestly believe that Madarame should be rewarded for selfishly holding on to his unrequited love for his best friend's girlfriend for so long? Because I really, really don't. I think he should move on and find love elsewhere, and, for once, confidently decide to stop clinging onto a worn-out fantasy.