It could strengthen Harry's relationship with the Hogwarts faculty. Since Flitwick is taking the time to train him, Harry might feel more connected to the school and its teachers. This could lead to him having more support from the faculty as a whole.
Well, in fanfiction, Flitwick could be portrayed as having a deep understanding of ancient protective magic. He might use this knowledge to create a sort of magical perimeter around Harry. He could also enlist the help of other magical creatures or objects within Hogwarts that are known for their protective qualities. For instance, he could get the help of the house - elves, who have their own brand of magic that could be used to keep Harry out of harm's way. And he may constantly be on the lookout for any signs of danger directed at Harry, using his magical senses to detect any malicious intents.
One possible plot could be that Flitwick focuses on teaching Harry advanced charm spells. He might see Harry's potential and take it upon himself to train Harry privately, away from the prying eyes of Snape or other potentially hostile teachers. This could lead to Harry having a new set of skills that come in handy during battles.
Well, it can really shake things up. It allows for alternate outcomes and character developments that wouldn't happen in the original timeline. It also gives the author more room to explore unique plotlines and themes.
It might make his relationships more interesting. If he reads fanfiction that has unique takes on his friendships, like a story that shows a deeper bond between him and Hermione, he could be more conscious of those relationships in real life and try to strengthen them further.
It might make her more mysterious to her friends at first. They could be both intrigued and a little bit wary of her ability to change her appearance. But as they get to know her better, they come to accept and even rely on it in some cases.
His friends might find it a bit odd at first. Some of them could be put off by his constant need to clean. For instance, Ron might not understand why Harry is always tidying up their dormitory and might feel like Harry is being too fussy. However, others like Hermione might appreciate it as she also values order and cleanliness.
Harry might develop a different set of values. Flitwick has his own way of looking at the wizarding world. Under his care, Harry could grow to value knowledge and magical finesse more than he does in the original story. This could lead to a Harry who is more diplomatic and less impulsive when dealing with other wizards and witches.
It could have a major impact. Harry's relationship with his teachers might also shift. Snape, who caused the transformation, might have some unexpected reactions to seeing Harry as a girl. Other teachers might treat 'her' differently too. And as for romantic interests, well, Harry might attract different people now. Some boys who never considered him before might start to notice 'her', which would create a whole new dynamic in his social life at Hogwarts.
The mask could potentially strain Harry's relationships. His friends might be worried about him using the mask and getting corrupted. For instance, Hermione could be very cautious and try to persuade Harry to get rid of the mask. This might cause some friction between them as Harry might be more curious about the mask's power.
Well, if fem Harry is older, it might change her relationships a great deal. For example, in her friendship with Ron and Hermione. She could be more of a mentor figure to them rather than just a peer. Older fem Harry might have a more mature outlook, which could lead to some initial friction as her friends might not be used to this new dynamic.