Me I wouldn't, I have a small and lightweight rain cover that fits allmost everywhere.
"I was hiking through the Malaysian jungle (Tanah Rata, jungle trail maybe 9/9A) in flip-flops"
And I love to travle light and being barefeet, but I really would not recommend hiking in Flip Flops. I like protecting my feet from leeches and more importantly snakes, scorpions, spiders, thorny bushes and small holes where you can hurt your angles.