Leadfoot, I think there are two issues here. Keith was, I believe, thinking of waving the Pen around outside the Platy to zap the water inside, because the Pen won't fit in most Platy's. That won't work.

About your question.... There are three things that you need to watch out for with the Pen and flexible/foldable containers.
1) The plastic blocks UV, so don't bend the container.
2) The Pen radiates light out from the sides of the bulb and not so much the BOTTOM of the bulb. I was told that it's nearly impossible to guarantee exposure of all the water to UV, in an enormous container like a 2 liter platypus. The Pen only sticks down a quarter of the way or so.
3) Most neck openings are simply too small for the Pen.

Sounds like you'll be fine with the liter sized flexible Nalgene. Just don't fold it in half while zapping <img src="/forums/images/graemlins/grin.gif" alt="" /> That container is a good idea, actually, and probably a bit lighter than the polyethylene Nalgene I use now.