Lauren, it's very common for toddlers with Becker's MC to have the hypertrophied muscles...they get so musclebound they fall over a lot, but as they grow, it gets better. Right now he doesn't know how to stop and relax so he pushes against the stiffness and that creates a very powerful isometric exercise.
I agree about avoiding the medications until he's older. The epilepsy drugs can cause some personality changes, especially at such a young age, so I encourage parents to wait and use a different medication like Diamox or Mexitil later which would not have as much of an effect on mood.
If you haven't seen the letter for school staff on the main website that might be helpful for you to read. It gives some tips on coping with the myotonia. (The link is above the search box.)
I know it's hard to watch your little guy struggle, but many of us are grateful for what our condition has taught us. He still has wide-open options for careers (except the military) and since he has the recessive form, he won't have to worry about passing it on to his children. Just to be sure his future mate can be tested when they decide to start a family, but the chances are almost zero.
I think the most important thing you can do is not be overprotective, don't encourage a victim mentality (it's not fair!) and teach him to laugh at himself when his body does unpredictable and embarrassing things. Being open about our condition with others and keeping a good sense of humor goes a very long way to having a happy and fulfilled life.
My 5 year old daughter was diagnosed about a year ago. We also chose not to do meds for the same reasons you gave. I agree with Jan about the importance of staying positive and not letting them feel sorry for themselves! She is the arm wrestling champ in our house :). We notice she has a harder time when the weather changes for winter. Being nervous also makes her stiff. She loves the movie Frozen, so when she gets stiff she calls out "frozen"!:) There is so much they can do just by learning to warm up. I know its overwhelming at first, but hang in there! We remind her that God made her special just the way she is, and He does not make mistakes.