Everything I have ever read about prosphora indicates that white flour should be used to make the prosphora. This is verified by Father George (originally By then Subdeacon George Aquaro) from www.Prosphora.org
when he notes:No Whole Wheat Flour
Some people think that whole wheat flour is somehow "more natural" and therefore more appropriate for prosphora. Nothing can be further from the truth, and whole wheat flour should be avoided unless there is no other option.
First, whole wheat flour was never used in the early Church. White flour was always used, since it was more expensive that the brown variety and the loaf was quite literally a sacrifice for those who provided it. Second, whole wheat flour is merely the same grain as the white, except with the outer shell ground in with the kernel. While this has some nutritional value, you would have to eat a LOT of antidoron to get any value from it! Third, whole wheat flour is harder to work with. It takes longer to rise and creates less regular bubbling. Fourth, whole wheat flour makes a harder crust. http://www.prosphora.org/page4.html
He also cites:On Food and Cooking
by Harold McGee (this book is in cooking circles considered to be authoritative).
"After flour has been ground and blended to the desired mix of particles, it is treated chemically to accomplish in a matter of minutes what otherwise takes weeks. Bleaching removes the light yellow color caused by xanthophylls, a variety of carotenoid also found in potatoes and onions. The color has no practical or nutritional significance and is oxidized simply to obtain a uniform whiteness. Bleaching does, however, destroy small amounts of vitamin E in flour, which probably accounts for its bad reputation in some circles. For historical reasons, yellow coloration is valued in pasta, and so semolina is never bleached.
"Bleaching is often accomplished with the same gas, chlorine dioxide, that is used to age or "improve" the flour. But even unbleached flour has been aged with potassium bromate or iodate. Aging has important practical results. It has long been known that flour allowed to sit for one or two months develops better baking qualities; hence the practice of letting flour age before use (during this period, it is also naturally bleached by oxygen in the air). But done in this way, aging is a time- and space consuming, somewhat unpredictable procedure. Hence the use of chemicals both to accelerate and to control flour improvement. Aging effects the bonding characteristics of the gluten proteins in such a way that they form stronger, more elastic doughs."
So, what he's saying is that the modern bleaching practice is something like using dry yeast: the Fathers (or dare I say mothers!) left a lump of dough out to collect naturally occurring yeast particles since they didn't have little jars of Fleischmann's at the bazaar. When I was in Greece, I picked up on this when I noticed that peasant bread (using local flour) was indeed yellow. The island didn't have the modern facilities to age its flour with chemicals, nor did they have the inclination to risk letting their flour sit around for a few months and risk dampness, wild yeasts, etc. Mr. McGee also points out that this process improve elasticity in dough. This is extremely important in light of the alternative: crumbing! I know our parish priest dreads loaves that crumb, as it complicates his clean up and his efforts to appropriately handle the Gifts.
The Fathers don't discuss it simply because they took it for granted. White flour was the best for what they needed it for, and people wouldn't think to bring anything lesser as sacrifice. White flour, in which the outer bran has been polished off, dates back long before the birth of Christ. Asians typically eat rice with the bran polished off (white rice) and have done so for thousands of years. Around 400BC, Hippocrates wrote of the differences between white and brown flour. Around the same time as Aristotle, the culinary writer Archestratus sung the praises of white bread from Lesbos in his book, Gastronomia (McGee, p. 282). McGee goes on to say that classical Greeks had a deep affinity for white flour.
The use of white flour is also witnessed in two other ways: the ecclesial arts (which spared no expense, since the process of polishing off bran is more costly in the loss as well as labor) and the witness of monastic centers (who both rigidly hold to the practices handed down to them and use white flour). Unlike the West, technology and science has never posed problems to our Faith. We thank God for the conveniences! There is "unbleached" white flour which is available in most markets with a decent selection, but, as you read, the process is much the same as it is for the bleached.
This may be located at http://www.prosphora.org/page8.html
Father George answered my questions that were similar to yours, I hope this will help you in your understanding as it did mine.