I think the alignment piece you originally referred to is a huge benefit of the aiming "systems" out there. 90/90, CTE/Pro1, SEE, etc. all recommend or even require the user to follow prescribed steps to start from a specific alignments, move down into the shot in a certain way, etc. All of these steps, whether purely mechanical or laced with "feel" (like pivoting etc.) are still steps and through training become subconscious and very repeatable.
I was pretty consistent before messing with aiming systems, I'm even more so now. I wouldn't dream of stepping into a shot without being aware (at least subconsciously) of my back foot placement and initial alignment. I agree with one of CJ's recent posts, you start out very mechanical during training but to reach your top gear you eventually need to let go of the steps and just perform them, only going back to the very mechanical approach when working on something new or fixing a flaw.
People do perceive things differently, that's why it's good to have as much as knowledge as possible when teaching, or even for your own use in double checking your aim etc. I find using discrete points like centers, edges, even shadows, etc. easier to see than a point in space or on a portion of a ball that I can't see directly, but that's just me, and probably why when I gained the information presented in the systems I took to it. I was already a pretty good ball pocketer before, it's just with the systems it gave me even more confidence and I felt even more locked in, leading to better results. I would still teach a new student the basic ghost ball concepts before overwhelming them with throw, cling, systems, etc.
After over a year now of experimentation and using the systems I agree that the pivot portion has a "feel" component to it, especially as sometimes described. In practice the moves can be done repeatedly and consistently and thus to me can be legitimately part of the system. I certainly don't feel like I'm dialing into the shot visually, once the initial pocket is chosen and the lines are sighted the pivot just happens with almost no visual reference to the object ball/pocket path. However it happens, the feeling I get of being completely locked in can't be ignored and the results confirm those feelings.
Scott