I have been diving only sidemount since I completed the course this past April in Florida. I came back to Missouri and took another couple SSI courses, one of which was navigation. I showed up in sidemount at the lake for the checkout dives and the instructor asked if I had a standard backmount rig with me....I didn't. He didn't seem happy but let me complete that course in sidemount. They don't see a lot of it in Missouri.
I had signed up for the Stress & Rescue course and asked ahead of time if I could do it in my sidemount rig. I was told no.
There is nothing about the nav course that couldn't be done in SM. Not sure why they had a problem with it. Not sure what other courses you were doing but all the ones I can think of would not be an issue in SM.
S&R in SM should have been allowed. First, there is no restriction on it. Second, it's only a small change in what needs to be accomplished. You would certainly find how easy/difficult it is to remove your tank(s) in a rescue situation. Plus, it can be instructive to the other students ("what would you do?" "what would be different?") Heck, if I were teaching it, I would have you as a victim after they did the skills with a backmount victim.