First off the main flaw in this entire argument that I have seen is expecting logic to explain any rules system perfectly.
Now, as for why individuals are flat-footed until they act in the frst round, I submit the following.
Prior to the initiation of combat, opponents may be aware of each other. In theory everybody is ready for something to happen. Weapons may or may not already be drawn. People are twitchy, but so far nothing has happened. You are looking at your opponents, you are looking at your companions, you are waiting for a signal, you are thinking about which one you should attack first, you are wondering which one will come after you. Once someone declares an action, suddenly everything roars to life. In theory, everything happens at once, in the game, there has to be an order. That would be the initiative order. The first person to move/act has the advantage. That person (let's call him Joe) was the quickest, most ready to respond to the twitch that initiated combat - even if the person who declared the initiating action (Mike) has not performed the action yet because of a lousy roll. Joe notices Mike starting to make a move. Joe pounces - Mike, whose mind was busy stepping off to his left and swinging his sword at Harry - his declared action that hasn't yet happened - is basically caught unaware. Mike thought he had the drop on everyone and was focused on what he wanted to do. He was wrong. Mike is caught flatfooted. It was impossible to think about every possible situation, so his mind was focused on a very limited set of situations. Up until that moment when he twitched, Mike was standing in one small spot or moving in a predictable manner, allowing a nice easy targeting of where his vital organs were or would be in a moment - if someone is fast enough to take advantage of it.
Now, once that first round is completed, the idea is that everyone's mind has gone into a mode where you are constantly aware of the tactical situation around you - your world has contracted to the area immediately around you. The number of likely possibilities has contracted as well. The opponent across the room with a sword is no threat to you, the one five feet away with is. You dodge a blow from one opponent while trying to attack another. Someone races by you, you get to take a swing at them. Now a person with Combat Reflexes is a person who is, in my opinion, trained to always be in this second frame of mind. Most people are not able to always be "on" like that.
As for readying out of combat, by the rules you cannot. You are premitted to ready an action on your turn in the initiative order. If someone goes before you are able to ready an action, you obviously cannot ready that action in time to respond to them. A person with a readied action goes on the initiative count of the person who triggers the readied action. If the action does not happen, the person with the readied action retains the same initiative count and on that count can change his action, or maintain the readied action. So, what is the initiative count of a person who readied an action outside of combat? They don't have one, yet. Should they not be permitted to have one until their trigger action occurs, or at least until the first round is completed - in which case they are essentially flat footed except in the case where the trigger action occurs.
Edit: I just reread that last paragraph and all I keep thinking is "how much wood can a woodchuck chuck..."
