I realize the flute's an apple and the horn an orange already. The point I was trying to make is that when it comes to timbre control and dynamic control, the flute and horn have some remarkable parallels. If you read the section from Philip Farkas' horn book dealing with the debate between F horns and Bb horns, he describes higher keys as being piercing and shrill, and hard to play softly - almost exactly my experience with short and thick flute bores. He describes low horn keys as (exact quote!) "thick and muddy, resulting in poor flexibility" - just like the longer skinnier flutes tend to do.
This means that as you move to higher flute keys, the absolute diameter of the bore should get smaller in tandem. And the lower flute keys should use a wider absolute bore diameter.
It doesn't take a rocket scientist to conclude that maybe higher horns should use narrower tubing and low horns wider tubing. Of course, it's unreasonable to use a separate horn for every single key signature, unless you bring a wheelbarrow out on stage filled with all of your umpteen horns so that you have quick access.
So you need to use crooks. However, while it may be unreasonable to own a dozen separate horns, it's not nearly as cumbersome to have three of them for high, middle, and low keys. Only trouble is that the crooks won't be interchangeable from one horn to another because of the bore disparities.
Even that might not be too much trouble. Crooks can be made to be very compact by coiling them. And even if they weren't coiled it would still be pretty reasonable to go down a major third. Look at it this way: the third valve on a modern horn drops the key by a minor third, and the entire extra tube length is confined to the third valve slide. A major-third slide for the F horn is only slightly longer than this. If you make it a bit longer still - voila! You have a major third crook for natural horn in D that will take you all the way down to Bb basso. If the high horn's highest key is C alto, the middle horn G, and the low horn D, all you need is three crooks for the high horn, four for the middle and three for the low.
It gets better still if you exploit the "trombone effect" by making the sliding part of your crooks fairly lengthy. One crook could cover the minor and major second and another the major and minor third, reducing the total number of required crooks to only 6. And the slide trombone was the first brass instrument ever to attain chromatic utility, so the knowledge and technology was definitely around by the second half of the 18th century.
Some purists may argue that the slide trombone doesn't count as a "natural" brass, because it's capable of chromatic musicianship. But the defining feature of natural horns is the lack of valves, not the lack of chromaticity. It was technology that brought the valved horn about, and long-slide crooks are much lower tech.
This is why I believe knowledge was the limiting factor. They knew that longer tubes have a lower pitch/key and shorter tubes a higher one. I guess it MIGHT be a possibility that they weren't much aware of the role that bore-length ratio plays in tone color. Or maybe they were skeptical that it would work, for much the same apple-and-orange reasons you gave. Or that the "trombone effect" would reduce the number of required onerous crooks. You have to put 2 and 2 together to come up with the conclusion I just did. But it still seems they would have to be pretty doggone ignorant in order for NOBODY to see this.
As soon as a few horn theorists reached the above conclusion, they would almost certainly want to do some experiments. Even if composers started implementing the horn key disparities into their compositions and made peace with them, others would most certainly have seen it as a significant problem, one that deserved a solution.
Of course, all of this would only work if the bore-length ratio really is the main culprit for tonal variations.
