As a trainer/behaviorist I never recommend free feeding. For the reasons stated by Julie and Jean, plus he who controls the food controls the dog.
If a dog can get food anytime he wants, he has no incentive to obey you at all. Why should he? After all, he has food, water, toys and can get your attention anytime it wants it. But, if you control the food, the dog understands instinctively that YOU are leader of the pack and you are in charge. His role is to follow not to lead.
Also during housebreaking it is vitally important to know your dog's eating/pooping schedule. If you free feed, you will have a very tough time of it house training your dog because you won't know when he ate and when its time to go out (on schedule since puppies can't tell you yet when they need to go out).
As for being able to take the food away or get near the dog when eating, as Julie said this is a management/training issue, not an effect of free feeding or not free feeding.
You can work with your dog at meal times first by taking a small cracker and letting the dog think you are taking it from HIS BOWL, eating it in front of him and THEN putting his food down for him to eat. Leaders always eat first. This puts the dog in the right frame of mind and helps him to understand that you are in charge of the food and the leader of the pack. More incentive for the dog to want to learn, please you and obey.
Put a bowl of food down on your lap. Call the dog to you and let him eat it from the bowl as it is in your lap. Occasionally take the bowl away and then give it right back to him. Stick your hand in the bowl and fiddle with the kibble when he is eating so he gets used to people handling his food. Hand feed a little bit of kibble, then put the rest from your hand back into the bowl and give it to the dog. Pet and soothe him as he eats as well so he becomes accustomed to being touched when eating and doesn't become afraid.
If the dog is eating too fast and throwing up food, put a rock or some large object in the bowl (a ball) and let the dog eat around the object. This will help slow down their eating/gulping of food.
Good luck.