Are you saying that during the time she was Secretary of State the agency did not make and preserve records?
You stopped reading the law early. It's not just keeping records but making them available. It's the latter part she did not do. I'm not willing to give any government official two years after they leave office to make good something they should have been doing daily.
Her emails were in possession of Hillary Clinton and not the US Government. By not turning those records over to the US Government she was in violation of those sections every day she was in office and the two years after until she turned them in. The part she failed was the latter part of 3101 where it states "... and designed to furnish the information necessary to protect the legal and financial rights of the Government..."
In doing so, the government was not able to fully comply with the FOIA act put forward to them. Again, to the government they never existed. And they would have never existed until someone in the National Archives asked for them. By keeping them away from the Government and the people of the United States, she was in violation of the law as she had a proactive duty to provide them.
Since her system did not satisfy the requirements of 3101 that the records be available to the government she automatically failed 3102. By keeping the records for years after she left office and never once providing the records while in office she failed 3103 and 3104. And by playing keep-away from the archivist, there is no way she could meet the requirements of 3105.
Now, assuming that she kept perfect records, would be so kind as to explain why you think that her keeping the records on her servers and her servers alone meets the standard being "... designed to furnish the information necessary to protect the legal and financial rights of the Government and of persons directly affected by the agency’s activities."
And if it did, why did the government respond to a number of FOIA requests that the information they are now providing from her emails didn't exist at that time while still meeting the requirements quoted above. Either her system furnished the records an the Government lied about not being available or they weren't available because her system was not designed to furnish the information necessary to protect the legal rights (FOIA) of persons directly affected by the agency's activities.