Thanks for the helpful replies. The water bottle idea is pretty clever and I'll be sure to exploit that at some point in time. I may end up getting a handle bar bag for some of the weekend rides where I plan to stop along the way.

I ended up picking up a Novara Small Wedge Seat Bag from REI. While I was there I looked at what other bags they had available. The Topeak small wedge was still too unwieldy as far as I could tell (with the quick release, no strap versions were available) and the micro won't fit a tube, small patch kit and the Alien II. But this Novara wedge is perfect. It has a twist release and after mounting it on the seat rails I zip-tied a Cateye LD-600 to the LED loop so I still only have one thing to take off the rear of the bike (bag+rear blinkie vs. just rear blinkie).

I can jam a spare tube, patch kit and multi-tool in there and probably have a tiny bit of extra room for something else, perhaps a couple of bandaids/tiny first aid kit.