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I think that what threw Madison's calculations astray was the advent of party politics - such things as political parties within the United States were yet to form and Washington, for one, hated the very idea

Washington did indeed hate the very idea of factions in government. Madison however was a very strong advocate for them thinking that they would serve as yet another check on runaway government so I doubt very much that his thinking was overtaken by them having arisen.

Yes, but we're considering what his thinking was on 5 February, 1788. We have the advantage of two centuries of hindsight; he and Hamilton and the rest were still fumbling in the dark when they wrote these things. The Madison who watched Washington burn while he was President was a very different man from the one who was still struggling to convince his countrymen to ratify the Constitution.

It is a moment frozen in time, for us solidified around these seed crystals of text that were for the authors mere letters to New York papers and yet so desperately important both to themselves and to the nation that was very much yet to be born. Nothing was certain to them. To imbue them with powers of clairvoyance and hold them responsible for the outcome is, I think, a little unfair. Enough to respect them for recognizing those things of which their flickering lanterns gave them a glimpse.

I'm afraid that a closer reading of #50 is going to force me to concede the point - Madison did at least suspect that party would be a factor in the federal government at this relatively early date. He might have been a bit surprised at what decisions it would eventually force him to make, and where it would end him up. That's a topic for a later discussion, but your point is most certainly sound.