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The more we understand the dog the better is for making a plan. I want to point out the confidence issues you are seeing with the pup are not necessarily from something the breeder did but mostly genetic. So she is not likely a case that needs rehab of some sort, she also is not really any kind of “reject” so to speak from a natural perspective. What you are seeing is mostly natural behavior for less domesticated dogs.
What happens with German Shepherds is that they are very very prone to what I call reverse domestication, in my OPINION most likely because they have more ties to recent wolf genetics in them. So when you see a 4 month old pup that is happier in her “den” and feels vulnerable when not close to mommy it is actually very normal “wolfy” behavior. I know from breeding shepherds that the first thing to go out the window when a breeder doesn’t pay attention is the “nerves”. When we see dogs that don’t seem to care about loud noises around them and new surroundings we call it “good nerves” but in actually it is humans selecting for a sort of numbed out and suppressed flight reflex. German Shepherds also have one of the strongest pack drives out there. In certain lines it is very very high and this is a good thing and a bad thing depending on perspective and situation. Dogs with high pack drives tend to be the most loyal and protective of their owners. You are seeing some things that are good for many purposes, BUT if you try to fight mother nature with her and try to make her into a dog that is content to be by herself, especially at 4 months old you can do more harm than good at this age. Instead of trying to go to the extreme of keeping her by herself, I have found it always better to go the other way around and allow her to be close to you and then slowly getting her used to more alone time as she gets older. Being separated from people and other dogs will be especially traumatic to a puppy at this age that wasn’t too long ago with her litter mates. I would suggest checking out this post here :bringing home a new puppy If you go the wrong route with the puppy the constant anxiety will be far worse in the puppies mind than a single swat with a slipper. The submissive urination is normal at this age and a sign of respect. It should go away with age as she learns you a fair and predictable. Never ever act as if you take notice of the submissive urination since it is involuntary, and if she senses you are not happy with it, it will have a snow balling effect.
In a nutshell, even though she might not be the typical German Shepherd you signed up for, it is normal for her and accepting that (hence are tagline “We welcome these dogs as they are..”) if you go with mother nature every dog shines in the areas that are unique to them. The wolf I was training basically acted the same way you are describing her, just more extreme. She would go through a wall to get to her mommy and stay with the “pack”.
