I'm going to answer first and then read the other answers, so I might have to add something...
The best way to prevent genetic flaws (at least ones that lead to dog aggression) from becoming a problem is proper socialization at a young age. As you suggested, puppies that are well socialized with other dogs, even if their breed tends to be dog aggressive, can learn to get along well with other dogs.
But, and this is a big but, not everyone owns their dog as a pup. Also, the majority of dog owners only see their sweet little puppy and do not realize that most dogs do not show serious aggression or really come into themselves completely until they are a little older. There are also all those dogs that are socialized well and STILL don't get a long with other dogs.
My Shiba/Corgi mix is dog aggressive with hyper, in your face dogs. He prefers his space, and if its not given to him when he gives a warning growl, he will bite. He was well socialized, and he absolutely adores dogs that play at his pace.
I see it as MY responsibility to keep him under control, to understand his body language, and avoid him running free with dogs that I KNOW he will not play well with. Whether or not his aggression is a genetic flaw, I will never know, but considering he was from a puppy mill raid, I wouldn't doubt it. Again though, its my responsibility to know my dogs personality, his triggers, and to either keep him away from them or have him under my direct control whenever there is the chance we will cross a trigger (meaning leashed with his prong on).
So overall, to answer your question, from my limited experience, there is only so much you can do. There are steps that can be taken to prevent a seriously screwed up dog, but whether or not a dog with a genetically flawed temperament can do whatever a completely stable dog can do, I am not convinced of. If you are looking for a dog that can go to the dog park with you every weekend, don't pick a breed that tends to be dog aggressive or go to the shelter and rescue something you aren't prepared to deal with.
Yah, I'm glad I'm done so I can read the other answers ;-)