We have reasonably nice records of interviews that have been done in the last decade or so that give us a limited insight into *some* of what happened in the early days, but we're not totally clear. Some things we know happened; some things *probably* happened; somethings *maybe* happened; a lot we just don't know.
In terms of Ueshiba's "internal" body skills compared with Takeda's, we'll probably never really know. Note that Ueshiba turned out deshi and other students who "did Aikido", but they certainly didn't use the internal skills in exactly the same way Ueshiba did because Ueshiba simply didn't teach those skills. Abe, Tohei, and others have publicly stated that they got their training and insights into "internal" skills from other sources. Their Aikido is similar to Ueshiba's, but in many ways it is quite different.
My grasp of the skills that Tohei uses is that yes, they are based on the same general principles as all the other "internal" skills found in India, China, Japanese other arts, etc., but they take a different direction and emphasis. Takeda certainly had some "internal" skills, but those too were borrowed from the general source and were not something that Takeda discovered himself..... were these the same skills that Ueshiba wound up with or did he simply get his version through other sources and his own understanding? Should we constantly point out that Takeda wouldn't have an art of his own if he hadn't gotten the knowledge of internal skills from one of his teachers, or can that be mentioned as an obvious point not worth constantly belaboring. I know the love I would engender if I went on a Daito-Ryu list and kept bringing that same point up endlessly.
Unless we were there... which none of us were... many of these questions and their subtleties will never be fully understood. A good start for a real understanding might be approached from the idea that the Aikido of Ueshiba and Tohei was based on the ultra-relaxed faction of ki training as opposed to the harder "tension" training approaches of Shaolin. Maybe that would be something to bear in mind? Both approaches stem from the same core principles, but they're quite different in many ways.