What is semi-solo?
1. My rear panniers had rain covers and my companions had waterproof panniers (as were my front panniers). The high visibility yellow/green covers were nice for being seen and being waterproof was nice. That said I don't see why plastic bags wouldn't be fine. I never considered them as theft prevention and really just didn't worry about anyone snatching my clothing or gear even in the few cities on the TA.
2. I never did that.
3. We had no problems in national parks or other campsites except at Oh Kentucky! Campground in Berea (I don't recommend the place) where someone stole my cell phone while it was left unattended charging in the bathroom. When we went on side hikes in places like Yellowstone we just locked our bikes at the trail head with a cable lock.
In big bike friendly cities like Florence, Eugene, Missoula, Pueblo, etc. we were very careful where we left our bikes and always locked. If there is much chance of your bike and gear being stolen it will be in these larger towns. The larger and more bike friendly they are the higher the risk. That said 99.9% of the time you will be in rural areas or very small towns, we took no precaution beyond carrying our handlebar bags (in which we carried anything that was likely to be stolen such as money, camera, credit cards, etc.) with us in these small towns. In these towns with double digit populations folks don't lock their houses when they go on vacation, so I didn't see the point of locking my bike or worrying about someone stealing my dirty clothes and well worn camping gear.