Well, first of all let me go back to something that I don't think has really penetrated very clearly.... these skills aren't unique to Aikido nor were they unique to Daito Ryu, nor are concepts for different styles/factions unique, and so on. Notice that Tohei has a separate ranking for the ki/kokyu skills outside of his Aikido ranking. Note that O-Sensei's cryptic quotes are obliquely sometimes and specific many times in quoting standard Chinese directions/admonitions about these skills.
When people start talking about "ki" and they have Yin-Yang dichotomy and "A-Un" and Five Elements, etc., we're talking about the same basic skills with the same basic rules and principles. Some Koryu or Aikido faction that uses different techniques and applications, that's fine but the basic ki skills by necessity must be the same, depending upon how purely they're done.
Most of the differences you see and hear about in the Aikido discussions are due to some differences in approach to technique or are due to different training approaches for the skills or how complete those approaches are. Let me give an example of what happens (this is true historically in many arts, going back in martial history where the ki/kokyu/qi/jin skills are used).
Say someone learns some rudimentary jin/kokyu skills and develops a fair amount of power and ki-blending, but they still use a lot of arm/shoulder, never fully learn to use the dantien, etc. Their techniques will reflect that incomplete acquisition of skills and someone in a related school may note that there is a difference in the way the techniques, trainings, etc., are done. That doesn't mean that the basic principles of the ki/kokyu skills changed... the differences are simply a result of how well the skills are fully known, etc. So I tend to dismiss this worry about "Aikido-related differences" and so on. The basic principles (the ones Ueshiba quoted from the Chinese classics and that many other style use as a settled codification) are the same.
Using the above example of someone who has incomplete or not-completely-understood skills, let's continue with the scenario in which they still use arm/shoulder, don't really know all the ins-and-outs of the hara/dantien usage, and so on. They practice in their own way for a number of years and they imprint this incorrect way of moving with the kokyu/jin skills. They still have power, etc., but they're limited (and there are other complexities too involved to go into in this post). All the students learn to move in this incomplete way and their techniques all follow suit. Can they change over to a more complete understanding? It's pretty hard to do, historically. There's a saying about this in Taijiquan that says: "Taiji is easy to learn, but difficult to correct". As proof, go look and see how many "senior Tai Chi instructors" don't really have any power, etc., because they learned and practiced some bogus method and could never change over, even after they meet truly qualified teachers.
So yeah... there's a lot of complexities to consider. Still, since all of this is just starting out, some of the results aren't going to be seen for a few years, but it'll be interesting to watch.