Neat idea! While I would not consider it to be any more sanitary than just flipping them over... I like that it keeps the dust off so they look nice when you pull them off the pile to dip into sanitizer.
I always find myself rinsing the dust off the outside then sanitizing... this will definately help.
The only negative I can see would be if this traps moisture inside the bag, and creates humid conditons inside the bag that will allow molds to grow.
I am thinking just leave the bottom "loose" like you have and only cover the bottles after they have dried... and it makes for the perfect dust cover....
(Now if I can only find a garbge bag big enough for my couch to cover them until company comes...
)