But can I mute them programatically without taking my hands off my instrument?

I don't understand the question.

You're not doing this on the fly.

You set it the way you want and then save the song. It will play exactly as you set it every time. No hands are needed.

Think of it like a MS Word document. If you center some text and make it bold and then save your document, the selected text will be centered and bold the next time and every time you open (play) the document.

You don't have to center and bold the text again every time you open (play) the file.