Aunt May was the most understanding woman Petra knew. She was kind and sweet and Petra didn't wish she was raised by anyone else. But she was terrified to tell Aunt May sometimes, she was Peter. Aunt May had always bought her girls clothes, but oftentimes when Petra hung out with Harry, she'd borrow his clothes (occasionally permanently). As much as Aunt May loved her hair, Petra insisted on keeping it short. It made it much easier to wash she told her aunt, leaving out that it was easier to look like a boy or a girl at any time as well. Petra loved aunt May. But she would never dream of telling her she was genderfluid.
She kept it a secret at school too, not that that kept Flash from finding out. She had kept it quiet for the first two years of high school, never going further than Harry's home when she was a he. But then junior year came and with it increased levels of teenager stupidity, and Peter started going more places with Harry. And then they ran into Flash Thompson, halfway through the first semester. He didn't believe it at first, that the skinny girl he had bullied for years was a puny guy too, and he used it to his advantage whenever he could, getting Petra to do his homework all the time.
Then the field trip happened; Petra was bitten and gained spider powers. Despite the incredible insanity the situation brought, Petra used the situation to her utmost advantage. She became Spiderman. An essential part of her spider suit was the binder she wore under it every time, and the small bundle she used to ensure the tight spandex suit didn't give it away. And so Peter was given a real life as Spiderman, as a boy. Petra was happier around Aunt May. And Peter saved the world. She didn't necessarily like that the he and she of Petra were so split into separate people. But it was better than being a girl all the time. And people recognized Peter as a boy. It was perfect. She even carried the practice of splitting Petra and Spiderman into two people when she moved into her own tiny apartment. It was just easier that way. Or so she thought.