disclaimer: i've never ridden anything longer than a fleche.

that being said, if flip flops are going to be a significant comfort and 'worth' the time cost to you, just go for it. for pretty much 95% of the traveling i do, flip flops are a must-have. drop-bag for the sleep controles?

also re: plastic bag storage for drink powder... i use bottles like this [Flat Oval Poly Bottle - 8 fl. oz. - REI.com], and they are practically 99.9% mess-free. use a funnel of some sort to get the powder in pre-ride, and simply dump/squeeze as needed. there are various sizes depending on your needs, but i like the oval profile as it seems more streamlined than something round.