Music boxes weren't programmable in the sense that they allowed for a different algorithm to be performed. They changed the timing of certain operations.
>Or perhaps only things that can have branch instructions count
The author identifies programmability as the most interesting metric, which creates a "computer". Branching is necessary for that but not sufficient.
Music boxes can have input data. Drum with notches is input just as cards with holes is input. They just do not have the other part of varied function.
It might not be fast to replace the input data, but it is possible.