The story of the younger son and older son is a contest of succession, which can only have one winner. They essentially had two different ways of reaching enlightenment. The youngest being chosen for his path via empathy/self-sacrifice is in line with traditional dharma transmission. I'm not a buddhist scholar, so please don't take this as an absolute proclamation, but I'm not aware of any non-human entities gaining dharma transmission. I know the reverse is true. But from what I know of buddhism, magical beings that have become bodhisattvas, did so on their own. If that's the case, it seems like they would have to have been his flesh and blood children, who perhaps inherited a curse or mutation from the juubi that transferred a little of the yin/yang chakra into each respective child. Or, it's also possible that he simply imbued them with yin and yang respectively, to um, get rid of it :I
I think that if they were made with creation of all things, then the story does as you say make some dramatic sense, in that yin and yang are not supposed to be separate, but are one and the same cycling forever, changing forever. That's the Daoist tradition anyways. Both sons as avatars ( sort of like minato ) for the yin and yang chakra would also fit thematically and symbolically. Part of why I feel it's more likely the later is that the emotional stakes are higher. There's countless succession stories like this where a younger son is chosen over the older son and a feud is born. The most famous in the west being Cain and Abel. Not only is the younger son's way rejected, but you could even say his birthright was also taken, as the oldest is usually given first dibs. This backdrop disappears if they were artificially created at the same time. If that was the case why even call them older/younger. But, it's not like I think that legends are sooo accurate anyways. As if these technical points and accuracy would have survived in the story till now, however it is supposed to be straight from SO6P tablet.
Side note of interest: Juubi was (I assume) forcefully taken by Rikudou Sennin and they never understood one another. Then he split them into the Bijuus at the end of his life, where they became separate individuals, it's not clear they have a memory of their time as the Juubi or not. I'll assume not. So a buddha by force, not acceptance as Siddhartha versus Mara. This is how I believe Naruto will surpass Rikudou Sennin by accepting the Juubi, giving atonement.
