Yet IN the Trekiverse--in that particular context--I think there's an argument to be made that the way the Progenitors programmed their children gave them a deep need FOR hybridization to be possible, and one that would be most pronounced in a civilization like the Federation, whose culture mirrors what the Progenitors had in mind and sees people
past racial boundaries. These races are not only programmed to have similar basic builds...with few exceptions, humanoids seem to be programmed to have similar instinctive facial expressions and gestures, and even though there are certain modifications, similar motivations. They are expressly made
by the Progenitors to have the potential to identify with, like, and even love each other. Given that, I think that they would feel deeply driven to find the means to be able to have children together when they feel drawn closely enough to each other.
If we took out the Progenitors, and had only convergent evolution without any guidance, than I strongly doubt such attraction would exist, or that ANY kind of interbreeding would be possible. But, when we consider that the Trekiverse species were programmed for it to be possible, and that in a number of cases they are biologically of the same genus, it makes sense from a storytelling perspective.