The thing about bungees is that they aren't ideal. It should be possible to make something custom that works better. But the bungees is a non-custom off the rack item that would be my second choice over something that was purpose built. I think fearmongering about bungees getting caught in the spokes doesn't serve any particular purpose.

The thing about rigging is that little subtle death traps are everywhere. Keeping it simple and proven is part of the key. After bungees, we get not one universally superior product we all agree on, but 20. Each one will seem safer because it would take maybe 20 times the accidents to raise the alarm to the level we get from the more popular bungee. There really isn't any reason to believe that bungees can't be improved on, but there isn't any reason to believe the new products will be safer until years have gone by and millions of miles cycled. I would have no problem believing that there are more convenient and high quality products that provide a "better user experience". But whether they will never lock up a wheel is another mater.

Also, the OP mentions an oversight, but the other thing is the size of the package. I mostly bungee a tent and sleeping bags, these items are pretty easy to get into a routine with compared to oddball packages. I do use bungees on those also while touring. Normally stuff like surplus food, but that is where the bungee versatility comes in.