I think it is a good idea to put the stuff in the bottle. If you get a source of water to fill the bottle, you can always give the bottle a decent washing first with clean/boiled water.

I echo the comments of adding a small waterproof bag of some sort folded into the bottle. Maybe include a small stuffbag as well. They don't take up much room. Then, if you need the bottle, you will have your items in a waterproof bag inside the stuffbag, which can be placed where you need it or carried in a cargo pocket, or what-have-you.