Re: "Hidden in Plain Sight" - Shinkage ryu menkyo
It should be clear that a lot of things we will ever know for certain.
What we do know is that:
Ueshiba Morihei studied with Takeda Sokaku in 1992 and received the daito ryu kyoju dairy and shinkage ryu certificates. The second certificate was regarded by Ueshiba Morihei as a ju-jutsu certificate (if I understand this correctly). For me this implies that Ueshiba Morihei was taught something outside of the daito ryu kyoju dairy syllabus.
What we also know is that the corpus of daito ryu was not complete at this time as we know it now. The number of daito ryu techniques upto and including menkyo kaiden is given by Kondo sensei at some point. In the film rendezvous with adventure Ueshiba Morihei gives the number of techniques in aikido (which I think for him was the same as daito-ryu except for the change in execution of technique which Ellis has described in his book) as almost the same number.
Might the shinkage ryu menkyo merely be an attempt by Takeda sensei to certify some techniques that were later included in the menkyo-kaiden syllabus but for which he had no daito-ryu certificate at this point. As Takeda Sokaku was paid for each the technique the shinkage menko had to add something.
Another point is that Ueshiba Morihei felt he could given a menkyo-kaiden to Tomiki sensei en mochizuki sensei while still teaching daito-ryu (predating the menkyo kaiden of Hisa sensei). What would have been his authority for this but some certificate comparable to the menko-kaiden.