Just think of it this way -- the more you leave behind, the less you'll need stuff sacks!
When things are muddy, there also tend to be a lot of stream crossings. When I wore boots, I used to do everything I could to keep my feet dry, including spending ten minutes taking the boots off and putting them back on in order to cross. Now, I just walk right through wearing my trailrunners. They dry within 15-30 minutes depending on temperature and humidity (and sock thickness). This saves time, keeps me cool on hot days, and also cleans the shoes off. Just a thought.
Personally, I never take an extra pair of bottoms (shorts/baselayer/rain/ or otherwise) in the summer. I'd consider it in the Whites, but that's about it. I hike in non-convertible, lightweight pants and wear underarmour boxer-briefs below those (and Body Glide below those). I switched to non-convertible because the zippers add weight and I never hike in shorts, anyway. Between bugs, thorns, and nettles, pants are a much more enjoyable option for long hikes. If I want to take a dip, the boxer-briefs are fine. New England summer nights are far too warm to be wearing anything aside from the boxer-briefs while sleeping. Plus, you said you're a warm sleeper and you've got a warm quilt. I don't know where you're headed, but I can pretty much guarantee you won't need the extra bottoms.
The fuel bottles make sense to me. It's worth the .2 oz weight penalty or whatever for the convenience and simplicity.