Like @kurt.braeckel mentioned, with clip-in style pedals you get to practice all four pedalling quadrants when following Coach Chad’s drills. With flat pedals, it’s pretty hard to get more than just the simple push down, though you can refine your pedal stroke to include a bit of the kick/pull motion.
I know it might be more work and more expensive, but your option #1 seems to make the most sense. I’m a firm believer that you shouldn’t skimp on anything that affects your health. However, if after working with a professional, you believe that the static position on a trainer is causing your indoor woes, perhaps a rocker plate could be a good idea. Lastly, if your muscle imbalance is really so significant, option #4 is going to be crucial. I’m not a sports physio, but from what I’ve heard, you want your body to be pretty even/symmetrical or you’ll cause issues and pain. Best of luck!