The fact that animals might be thrown into close quarters for a short amount of time in an emergency like that does have risks (cannibalism, etc.) but I would think the animals would be pretty stunned to have any time to do much harm to each other and if you can get them somewhere quick and sort them out I think you could avoid something bad happening in the bags or containers.
In my case having people I know so close and my friend also being the one who babysits my zoo when I'm gone. I could have the animals to him in about 5 minutes and he'd be sorting them out right away in different pillow cases or containers. I'm lucky that I have help so close by.
Keeper of 5 snakes, leopard geckos, 1 green iguana, 20+ tarantulas, 2 dogs & a bunch of rats!