What about in the days of the samurai and the 'inner sanctoms' of the shogun or 'boss'. Isn't that where it originated? In other words it had an original purpose and was practiced. I also have seen Ueshiba doing plenty. Thus it has a history all of it's own and a reason. Seeing the reason is seeing the use. Swordsmen I am sure would sit seiza for a reason to do with these type of movements too.
Traditionally there was only a limited amount of movement around on the knees - nothing like the amount that is done today.
If you watch Ueshiba in 1935, or even when he was older, he actually doesn't cover all that much ground on his knees.
Also, if you've done it, there's a big difference between moving on your knees on plain tatami (which is what everybody used to have) and the modern canvas or vinyl covered versions.