I posted on this a while back, and also tend to agree that a cup hanging outside your pack in the open air is going to dry out. However, experience has shown me that a cup hanging from my pack out of eyesight on a hot day when breaking through thick chaparral, is very likely to be missing at the end of the day, whereas a thin rolled up bag used as a scoop wrapped around the filter will probably still be there since it's in a pocket on the pack. But I like the cup method personally, I find it easy to do, particularly with very low streams with little water.
Also, if you use the cup, then get all the water you can out of it, then rinse it with a bit of clean water, then dry that out, you have then diluted the tiny amount of drops remaining from the dirty water substantially. All it takes is an ounce or two swished in the cup after getting the initial dirty water out by shaking it. If you then shake it vigorously again, I believe there will be a tiny chance remaining that any organisms will remain in large enough quantities to matter. If you did that process twice, the dilution would be getting to be fairly extreme, since each time a few ounces are diluting a few drops remaining from shaking it.