Do experienced programmers achieve the ability to code instinctively or achieve a visceral understanding of a path to follow when deciding how to solve a problem? Certainly the ability to program does not rely on muscle memory other than typing or clicking a mouse, but I believe there are reflexes that are developed over time that aid with the ability to create an algorithm.
Learning to program is similar in some ways to learning a new language. There is the need to adhere to a certain syntax that can vary from language to language. Languages also have different built in structures and functions can change how the language is used. Even if you are experienced in one language, gaining a familiarity with the strengths and idiosyncrasies of a new language takes some time. Building that comfort level is in a way developing a mental muscle memory that allows the programmer to focus on higher level problem solving. Beyond programming syntax, there’s the need for software architects that can determine the shape of the the entire project or platform, and an even more intuitive sense is needed.