It isn't that I think the separation should be choice in 98% of the cases, just in a select few. I think for the most part we can come up with reasons for the races to be split so decisively. However, if we are going to have races that stem from the same base on either side of the line, then it is not outside the realm of possibilities that they are still genetically compatible, and when it comes to those children, I do see them having that moment of choice, if they are ever told that they are born of both sides. Side hating one another has never stopped rape you know :P All it takes is for one elf to rape another elf, and boom, possible pregnancy, and a child born from each side. If she comes to term at least. :P 

As for the black and white example, I see what you mean, but I can also see some mixes producing children that are not clearly one side or the other. For example, if say red dragons are Daywalkers, then a red dragon child, even if it had a black dragon parent(In this case a Nightwalker) so yeah, it has no choice. However if a Gray Elf as a Nighwalker has a High Elf child(Daywalker), they both share such similarities that the child could pass itself off as from one race or the other. That child, if ever told, would have a choice. Or, if the child makes a perfect mix of the two, say a high elf face structure with red hair(The hair of a sylvain elf), then the child would belong nowhere, and this would add a very interesting angle to the story should such children exist in their own underground manner :P

So, when I say choice, it is suppose to be a very rare and unspoken of thing, since I see most of those kinds of pregnancies being terminated early. For me it's a fun idea, but if you really don't want it I guess I can just let my mind think of these things and I just won't write about them. . . .*Sad face* :P