The short answers to your questions are the following:
The muscles work by applying force to the bones that they are connected to. The magnitude and direction (expansion vs contraction) of that force is determined by the neural network output. Internally they use the Spring Joint component of Unity's physics system, which essentially acts like a real spring. The muscles fire at a constant rate.
Thank you very much for all of your questions! (I've also seen the other batch but haven't had time to appropriately answer them yet) I'm currently working on not only a big update for Evolution but also a FAQ page on my website where I will try to answer all of these questions and others that I've been getting in more detail, so that I can then just link to those answers when someone asks them again. If you or your students have any more questions, just drop them here in this forum or send me an e-mail and I'll add them to my list of questions for the FAQ.
I'll let you know once that page is ready (I'm a little busy at the moment so it might take a while).