6) Tokimune was there, and he said "Hey, how about we teach these folks the Hiden Mokuroku like back in the day?"
7) So they studied the Hiden Mokuroku and produced the Soden.
I believe there may have been some normalization between the Takumakai and Tokimune's mainline group in the middle of the 20th centiury. Not sure where I read that but the two groups look somewhat similar these days. Pretty sure the Takumakai does todome now.
So the solution to the mystery of the disappearing todome could be a matter of political de-martialization. Or it could be an issue of Osensei eschewing the kata of Daito ryu and instead focusing on showing off the principals.
It could also be that the todome were not added in until later, too, I am not really sure.
The Soden was an effort to preserve the techniques of Sokaku Takeda photographically, and it has nothing to do with the normalization that occurred (but never really stuck) in the 1980's.
I don't think that there is a mystery, and that it's a very minor point to obsess over. Morihei Ueshiba taught it before the war, and he taught it after the war. Various people emphasize it to various degrees, and it's pretty much the same in Daito-ryu.