I agree that it generally makes more sense to use shutter priority when shooting birds in flight and other rapidly moving objects. However, my recommendation to use Aperture Priority is so you can master the relationship of that mode, Auto ISO and exposure compensation. The idea that you might do so in a week or two is far more ambitious than what I could accomplish, so it's far more ambitious than what I was thinking of for you.
It's clear from your post that you intellectually understand the relationships and how your camera adjusts the various settings when using Aperture priority, Auto ISO and Exposure Compensation. However, it's understandable that you haven't yet mastered how to practically apply them in the various situations that causes all of us to make compromises such as whether to use a slower shutter speed or a higher ISO. As an example, you mentioned that when the Auto ISO max ISO setting is 3200, the camera too often uses an ISO setting that is too high. The solution is to simply lower that setting. As another example, I'm getting the impression that you're not aware of how your camera has changed a particular setting until you look at the metadata when ideally you should be carefully watching that information in the viewfinder. That's the sort of thing that takes practice, practice, and lots more practice.
Getting back to the concept of mastering something rather than trying everything, I also think you're trying to do too many types of photography. It takes lots and lots of experience to master either landscapes or birds in flight and I'm referring to far more time than a few weeks. Yet you're trying to do both at the same time, constantly flipping back and forth between them. Heck, it takes weeks just to fully understand the intricacies of a particular lens, especially a zoom lens, to the point of having mastered it. Yet you're constantly changing lenses because you're also constantly changing the types of photography.
Again, your process doesn't have to be as difficult as you're making it. If you can't be happy sticking to one type of photography, one combination of settings and the like for at least several months, my vote goes for being happy. However, if that's the case, understand the compromises that you're making. Also understand that flipping back and forth between various concerns brought on by shooting in such different situations using different combinations of settings, focal lengths and the like makes it much more difficult for people to make effective suggestions that will have long-lasting impact on your photography.
Just my opinion.