"I worried about where I'd store everything while I was using the bottle, but that's what pockets are for. Or, in my case, the rest of the BOB. "

Store a 1 gallon ziplock in your bottle. Put everything in the baggie and then you can use your bottle. Baggies tend to be short term solutions so you might think about either making or buying a nylon stuff stack the same size at the bottle with a belt loop sewn on the side. Remove the contents from the bottle and put in nylon stuff sack. Hang stuff sack by belt loops on belt.

Instead of belt loops you could use a carabiner. A much cheaper alternative would be a metal shower curtain ring. A 12 pack of shower curtain rings is only a couple of bucks and you could put a "carabiner lite" in all of your kits.

My Goodwill store had Eddie Bauer Nalgene bottles for $1 last week. Picked up a couple on the cheap. They also had off brand polycarbonate bottles for a $1.