Keep in mind that you don't want to have a completely sealed container for the filter's outflow.  If you don't some way for the air to escape as its being replaced by water, then you'll build up a positive air pressure in the container and that will ultimately curtail the water flow.  

One negative with using a "bag" container over a rigid one is that you'll likely fine the need to hang both the bag and the filter.  If I'm filling a nalgene-type bottle, I DO use the bottle adapter from my MSR water filter (which has an air-relief hole in the top).  However, more frequently, I'm just running water into one of my cooking pots.  Whether bottle or pot, they rest on the ground, braced with a piece of wood or rock to avoid slippage.  I adjust the bag up and down with a length of rope and a carbiner (which I unfortunately left on my last campsite on Batch last year).

dd

BTW:  My base camp filter got used for roughly 21 days of camping last year.