I believe a lot has to do with the temperment of the dog. I free-feed Phoebe, and she has done as the OP has said - assigned herself meal times. We always make sure she sees us filling her bowls, so she knows the food is coming from us (actually, I have the 5yr old fill the bowl, and make her "wait" before she's allowed to investigate it, so she knows she's lower on the pack order than he is - but that's another story for another thread
). BUT, my brother's LabX and my sister's BernerX would never be able to free-feed because they're gluttons.
Also, if you have a dog that has health issues, it's easier to monitor their food intake if you're feeding only at meal times. Finally, if you're still training your puppy, it's easier to know when they're feeding so you can judge when to take them outside for a potty break.
As for mixing food, I believe Trinity is right. If you're changing the quality of food, then it might be a bit much for your dog's system to handle all at once - kind of like if you've been eating a vegetarian diet all your life and then suddenly start throwing nothing but hamburgers down your throat. Also, some dogs are allergic to some food (like chicken), so it's a good idea to start slowly to see if there's a reaction before going all out.
HTH!