First, its incredibly rare for a free fed animal to not be overweight. I know its possible, but doesn't happen in most situations. Usually what happens is the owner (or possibly even the vet) doesn't know what ideal weight is, and thinks their overweight or even obese dog is fine.
When free feeding its more difficult to determine exactly how much your pet is eating and when. Its also more difficult to schedule bathroom breaks. Being able to notice immediately when something has changed in eating or bathroom habits can catch health concerns faster.
Feeding time can also be a great training time with your dog. You can ask for manners such as sitting and waiting to be released before they're able to eat. Some people use NILF techniques. Food is a great motivator, and you're tossing out that possibility to use feeding times as easy routine training sessions every day when you free feed. Its also more difficult to motivate the dog for training with treats when they're free fed, trainers recommend that the food be picked up a couple hours prior to a training session to ensure the dog has some appetite for the training treats.