There are a lot of antinutrients and stuff in grain that some people find difficult to digest. By pre-fermenting it, like with sourdough, makes it easier for our bodies to absorb the nutrition. I've also noticed, that many people sensitive to gluten can consume sourdough bread made in the traditional way. A short term rise like baking soda, doesn't give the same nutritional benefits.
Another way to think about it is to understand plants. Plants get used to an environment over several generations. I grow peas here, save the seeds, and in three generations, they are acclimatized to my soil. Humans are similar. For those of us of European decent, we have several thousand years on a grain based diet, we are genetically acclimatized to eating grains. However, our ancestors did not have backing soda or instant yeast, they used the equivalent of sourdough (wild yeast) to leaven their bread.
For better health in the sense of fermenting the flour through long proofing, I would think that it would be better to premix this and after proofing mix and add the other ingredients right before baking
I hesitate to agree with 'better' because I think that there are lots of different ways to do it that give different results. One way would work for you, one way might work for someone else. It depends on your body and what it likes. It sounds like a delicious idea, though, and well worth giving it a try. If you do, please let us know how it goes.