Maybe he doesn't fully understand his powers yet. Tony Stark is a scientific genius, but new powers might be beyond his current understanding. He could be worried that if he reveals them too soon, he won't be able to control them properly and might cause harm. So, he chooses to hide them while he studies and figures them out.
Pepper Potts. She is very close to Tony and knows him well. She might notice some strange behavior or small signs that lead her to suspect he has hidden powers. For example, he might unconsciously use his powers in a moment of stress or danger when he thinks no one is looking.
In fanfiction, Tony Stark might have enhanced intelligence powers. He could solve complex problems at a super - fast speed, like coming up with new energy sources in minutes. His suit could also have new abilities, like teleportation. For example, he could zap himself from one side of the planet to the other to stop a disaster.
He could have the power of technopathy. Since Tony is already so connected to technology, as a mutant, he might be able to directly communicate with machines and control them with his mind. This would give him an even greater edge in creating and operating his Iron Man suits.
One reason could be that he's frustrated with the leadership or the direction the Avengers are taking in the fanfiction. He might feel his ideas are not being heard.
He could develop technological - based powers. Since Tony Stark is all about technology, Harry might be able to manipulate and create advanced tech with his mind. For example, he could summon Iron Man - style armor just by thinking about it.
There could be an increase in his mental powers. The World Serpent is a very intelligent and cunning being. Tony Stark, already a genius, could have his intellect boosted even further. He might be able to predict the actions of his enemies more accurately, or come up with more elaborate and complex plans in an instant. His mind could also be more resistant to psychic attacks or attempts to hack into his technology, as the World Serpent is often associated with a certain kind of mental fortitude.
One great 'Tony Stark has powers' fanfiction is 'Powered Iron Man'. In it, Tony gains the power to manipulate energy on a molecular level. It makes for some really cool battle scenes where he can use his new power in creative ways along with his suit's technology.
One possible reason could be that he was forced to betray under some kind of mind control. Maybe an enemy like Hydra got hold of him and made him do things against his will. Another reason might be that he was trying to protect something or someone he loved in a very extreme way that seemed like a betrayal to others. For example, he might have made a deal with a villain to keep Pepper safe.
Another possibility is that he underestimates the importance of family. Tony has always been focused on his own achievements and the big - picture stuff. He might not realize how much his daughter needs him until it's too late.
Maybe he's too caught up in his work. Tony Stark is often depicted as a workaholic, so he could be so focused on his inventions and saving the world that he simply doesn't have time for his son.