Agreed on everything that has been said that it will help you to have this recognition for your achievements & that you shouldn't feel like a "fraud" because they ARE trying to recognize people who have overcome the disadvantages girls and women face in math and science.
Once you've graduated university, you wouldn't wind up putting high school awards on your resume. This is a cool thing now, but not something you'll always be forced to explain away or hide. In the short term, it CAN help you with applications from people you'll probably have to come out to anyway.
Here is my own personal sense - because this is something I grappled with in coming out:
Pre-transition, I had been 'praised' for a long time and viewed as somewhat remarkable, because I am very strong in math and math-oriented fields. Even within my chosen career, which is fairly mixed, I am on the more predominantly "traditionally male" side of the field/job/position in terms of the specifics of what I do. I felt uncomfortable for a long time being viewed as something special for having what other people viewed as more "male" talents and accomplishments. I worried about how I used to be a role model for young girls and women to show that anyone can be or do anything, and that transitioning was going to undermine that. I struggled with experiences like when I was basically out as trans in my personal life and a few months away from total full time/work and someone professionally - a very smart and outgoing woman I don't have much opportunity to work with - was going on and on to me about how awesome it was to have a "woman" who did what I was doing. I felt like such a complete and utter fraud.
And I think the worst of it was that I hated being "proof" that equality had been achieved, that women were being treated well, etc. Because I knew that my behavior was as stereotypically masculine as possible, and it wasn't because I wanted to fit some mold or succeed - I was just kinda being comfortable as me. So I was getting praise for fitting in, and being held up as some sort of example of what someone *could* be. It made me feel like I was working overtime to be the one to point out sexism or misogyny without really always understanding *why* and *how* me and my co-workers - or just standard aspects of our jobs - WERE excluding actual women.
My sense is that this might be part of what is troubling you: that your accomplishments in math and science shouldn't be viewed as them being 'successful' in improving math and science opportunities for the girls and women in your school.
Since I've come out, what I realized is that most people do NOT think, "Oh, you are a fraud! You pretended to be a woman. We should never have <honored you, thought you special, given you an award, hired you, etc>"
What they DO think is often: How hard must it have been for you to juggle your academic/professional/serious-minded work while you had so much personal crap to deal with!
But the harder part is learning to accept yourself as an actual role model and accomplished person even though it is NOT because you are a woman. It is from living as though people think you are, from being a role model to other LGBTQ and gender-variant people, and from prevailing with a perspective that IS unique about the need for greater recognition and more equality in the maths and sciences for ALL people who do not come from an advantaged position, whether through race, sex or gender, class, and so on.
