To my mind building "muscle memory" is what we do only in the very first beginning of practice. Maybe the first one or maybe two years. I think, it is only needed to be able to reproduce the external picture of kata to a certain degree.
But after that I think practice should be about feeling inside to connect the body of tori internally. And also about feeling outwardly to connect the body to aite.
So it is my experience that the image of building "muscle memory" is limited to the very beginning of practice.
My personal experience is that I am constantly and deliberately refining and re-training "muscle memory" on more and more sensitive levels, to the point where I am also re-programming instinctual responses.
Maybe I'm just a slow student, or it's just my different perspective of the training. I am definitely well beyond the first one or two years of my practice in both aikido or aikibudo.