I think you may have missed the point on a few issues here, and you've come very close to making some absolute statements (which is very dangerous). I agree about the drill manuals and their use (I have been frustrated for years that some manuals like Gilham's are ignored by many units, and that most units cannot form a correct color guard to save their lives). Even with the use of the manual you cannot say that every unit is going to do everything the same way. Many commanders change things to suit their needs, and some just have different interpretations of what the manuals mean.

example: In an article of the Journal for the Company of Military Historians (published between 10-20 years ago I believe), there is an article about the diary of a captain in a newly formed federal regiment. The captain talked about how he read how the manual (Casey's I believe in this case) explained the stacking of bayonets. While he was instructing his company in how to execute this command an officer from another company came over and chewed him out and said that is not how the manual says it should be done. At the battalion's officers' call that evening the subject came up and even with several other officers adding different methods, the colonel agreed with how the first captain taught his men to form a stack.
The Point: Just because the manual says something does not mean that everyone is able to comprehend it's correct interpretation.

You are correct that colors are very important for maneuver for battalions on the field, but as the battalion size decreases, so does the importance of the colors (ex. the use of colors for a 100 man battalion is not as critical as for a 1000 man battalion). Even larger units can be moved in the field with no colors at all (I've seen it done many times, it is not pretty and no where near as effective, but it can be done). And while you keep mentioning the drill books you have overlooked what they say and what I mentioned in my last post...when a battalion drops to below 5 companies (and there are several ways commanders can interpret this), the battalion is NOT AUTHORIZED to carry colors.

Now let's look at the units that do carry colors. There is a prescribed manner for them to be used (ex. 9 man color guard, 3 ranks deep of 3 men each). The front rank steps out 6 paces as you mentioned, but the battalion has no interest in seeing where the colors are going. The battalion is using those colors as there focus point for keeping their alignment...again as the unit becomes smaller this is much easier to do with and sometimes without colors. Now while those 3 men are in the advance you find the reason why there are 6 more men in the guard...let's call them place holders. They march in a direct line behind the front 3, and do not give ground to the left or to the right...the rest of the battalion takes their direction from them and should therefore not drift to the left or the right. All of the above mentioned is what happens in a PERFECT WORLD. What happens when a battalion becomes so weak that it's commander does not want the 9 man guard? What if the battalion is NOT weak and the commander still does not want a full guard? Look for example at every battalion in Pickett's division at Gettysburg. They are all fairly healthy in size and yet not a single one has more then 3 men assigned to it's color guard (many only have 2). Well what happens now? If this rank advances 6 paces as it should then the left and right-center companies drift slightly inward and leave no room for the guard to take it's proper position on a halt. Clearly the manual did not envision this situation, so something had to be done, and wonder of wonders the solution is not one that is written in the manual. Also, what of the 4th (I think it was the 4th, maybe the 3rd) PA Heavy Artillery stationed in Hampton VA in 1864. In a photo of the battalion we can see that the front rank of the color guard is 6 paces in advance of the unit while on morning parade (this cannot be because the manual says they should be in line during the parade). From the photo we can see that the front rank of the guard is 4 men not 3 (this also cannot be because the manual does not allow for it)! To have 4 men up front means the addition ranks combined would equal 12 men for the guard (impossible, the manual says 9)! And finally, with the four man configuration you have the 2 flags the unit carried right next to each other in the line (the photographer must have changed this since the manual says when 2 colors are carried there is to be a man between them).
Point: Things don't always go by the book.

When it comes to the colors for consolidated units I believe you must have been a bit busy typing and may have missed the point that the 47th and 50th VA were NOT consolidated units. So there are provisions for consolidated units and their flags, but they do not apply here.

And finally, I again agree that many professors just gloss over the military aspects of war. I see a great many college students and graduates come through our museum and not have an idea of how linear warfare works. Their professors came up with many notions that were incorrect, and a few so bad that it turned my stomach to think that these kids paid for an education that taught them garbage. However, through both working in a museum and through my studies for my degree (in Colonial American and American Civil War history), there are a few good lessons I have learned. Things almost never happen by the book. If you can't prove something happened doesn't mean it did not happen, but you have to diminish the chances that it happened (if a paper doesn't prove it, but an artifact exists, then the artifact is incorporated into a new explanation that joins the two). And not only do many people have different view of one thing or another in hindsight...in most cases they can't agree on them in the moment either (like interpreting a manual). The armies may live an die by the manual but they can very rarely ever agree completely on them (good thing that when VA started raising the first regiments they sent Instructors who were trained in a common interpretation of the manual, giving a better rate of uniformity in the drill).

Ken, I also agree with you.