About games in the community vote having already been in the flash sales or daily deals, and vice versa:
I think that, besides the fact that obviously developers+publishers+valve have an agreement on what kind of discount each game will have (which leads to a limited pool of games being discounted -> the same games appearing in different sales sections), ...wait that aside was too long so I'll just start again
I think that the community choices are one of the numerous ways in which Valve polls the Steam userbase to get more info about it, what it wants, how it works, and how to efficiently extract money from it. If a game has been on sale and it's voted for later in the community choice, that's a valuable piece of info that coupled with other experiments can mean that either the first sale wasn't highlighted enough, or the way sales work aren't clear enough for most people (even here we need flashy gifs to remind everyone that prices are the same in all the sale sections), or the game is just highly demanded. Plus, it gives info on what kind of games have the most involved audience, and I wouldn't be surprised if the later community choice selections were decided depending on the previous ones' results.
Reposting this link which went unnoticed but is super interesting (even if it's nothing new, we all know that Valve toys with our minds):
http://www.psychologyofgames.com/2013/07/the-psychology-behind-steams-summer-sale/