I've gone through life not being able to tell anybody everything about me. Everyone has secrets. Everyone.
I do understand the difficulty of holding onto such big things though. Just feeling like your in the wrong gender is so insurmountably difficult, that also having to keep it a secret does indeed make life even more difficult than it should be.
Drugs? I don't recommend them, from experience tbh, but you don't really need to tell your parents that you don't have anything against them. It's your business. But I strongly recommend you avoid.
Atheism? That's no big deal. Believe what you want to believe and don't let anyone shove their beliefs down your throat. I'm a humanist myself, I believe we can improve the world by helping each other.
The other day, when I had my first appointment with my gender therapist, was the first time I had actually told anyone in real life exactly who I am. For the first time ever, I felt complete. I hope you can find someone like that who you can completly open up to.
Sarah.x