I appreciate the upvotes and I do not wish to delete my answer, but I think it's important to note that @psosuna 's answer about pronouns as a "scale of humility" is more relevant toward understanding why pronouns are used the way they are in Japanese. My answer is based on the "gender association" that I was taught in college and my personal experiences in Japan, and my sense of what the original question poster was concerned about. psosuna's answer offers a deeper insight, and although I'm not saying "please undo your upvotes" (which I appreciate), I hope people will recognize the important point that psosuna has made clear about the Japanese language.
You definitely don't want to use あたし , as that is a pronoun used by people who identify as female. I can't imagine why your professor would suggest that you do, unless he/she is unaware of your gender identity.
僕 is a pronoun used essentially out of a desire to stress one's maleness, as あたし is used to stress one's femaleness. 僕 is also sometimes used by girls/women who simply see themselves as "one of the guys" and don't attach gender to it as strictly, but for this reason it is seen as somewhat uncouth.
You also hear younger boys using that pronoun more-so than older boys or men. This is because as Janusz said 私 is gender neutral and more polite, which younger kids care less about, and older kids/adults care more about.
As you care about making people aware that you identify as male, I think it is fine for you to use 僕 rather than 私. Be prepared for some people to think that you are simply being "rough" with your language though, rather than identifying as male, if you choose to refer to yourself that way. And be prepared for people not to understand your gender identity if you choose to use 私.
I want to apologize for not really being able to answer the point about ramifications, because I don't know what ramifications might develop from a non-cis-gendered man using 僕. As the comments say, Japan is more gender prejudiced than the West (which is itself still not great in that respect) so you can expect social discomfort from some Japanese people, especially older people, meeting people who don't conform to their biological gender. The use of 僕 will just be one aspect of the interaction that causes their discomfort though, so... :(
Further Edit: Thanks to one of your comments, I now understand a little better what one of your concerns is. The use of gendered pronouns in Japanese is not a guaranteed way to make people aware of your gender identity in Japan. Some people might get it, but most will assume that you are making some sort of linguistic mistake, and will attempt to correct you. Some few might simply think that you are trying to be "tomboyish" when using 僕. Unlike あたし, which is only used by women, transvestite men, and transgender women, 僕 can be and is used by some boys, some girls, some men and some women, so it cannot truly "hint" at your gender identity. I was recommending that you use it, based on the sense that it made you happier to do so, which I feel is a valid and sensible reason, despite the fact that it will necessitate conversations about language and about gender identity on occasion.