I just ordered a few different bags to try:
These have a flatter bottom which might fill the space a little better:
Keep your fish safe in our watertight bags. Our 3GSBW1 square bottom bag measures 6" x 4" x 18" and is ideal for transporting and selling tropical or ornamental fish. Expandable sides form a square bottom so your fish won't get stuck in any corners. This 3 mil polyethylene bag is made with...
www.clearbags.com
These seem to be the same dimensions that came with it:
3 Mil, water tight, ideal as a Tropical Fish Bag. Flat Poly Bags are the most common and economical bags for shipping or bundling products.
www.clearbags.com
I really do like the idea of just pulling out a bag and putting in a new one to start a clean new culture, but not sure I want to pay a dollar a piece forever.
Once I get these in I will update how well they fit for anyone that might want to try them with a DIY set up.