Do you really think that the bike with slightly longer or more flexible seat and chainstays is going to make an appreciable difference in your commute? You're using terminology that can make an appreciable difference in race situations, but commuting I find no real difference between my heavier, steel touring bike with longish chainstays and my aluminum 'cross race bike with shorter stays. Also the frame flex will unlikely be enough to save your wheel from banging straight through large potholes. Larger ires can do that, but it also helps to have a bit of technique.