It is not clear to me that it makes sense to talk about "overlap" for stem plots. stem plots do not have any inherent dot size, so points are either exactly the same or they are not.
If you want to test whether points are exactly the same,
mean(input_signal == output_signal) * 100
However, it would probably be better to use
TOLERANCE = 1e-8;
mean( abs(input_signal - output_signal) < TOLERANCE) * 100