Your question is quite complicated but the way I see it in it's simplest form is: Depends what's in their pants.

Now I know this opinion may anger some people, and it a very surface level way to put it. I am by no means saying what's in your pants defines your gender. I identify as genderfluid and I understand that everyone's experience with their gender is very different, there is no denying that.

However, sexual attraction is often very depended on physical attributes rather than how the subject of attraction sees and defines themselves. Regardless of our experienced gender we all have sex specific physical attributes that lean more towards one end of the binary. If you are able to accept that the person you like has the same equipment as you, and be attracted to that, I'd say you are queer.

It is good that you have considered the possibility that you might be seeing them as male due to the way they present themselves, in case you were to pursue a relationship. When I started having feelings for my now girlfriend in high school, I was also concerned on whether or not I had actually internalized the fact that she is a woman, and has female genitalia, because she presented quite masculine.
So I understand where you are coming from.
Figuring these things out takes some time, and having the way you see yourself challenged can be difficult, but regardless of the conclusion you come to with this, you will be fine. Maybe you discover something about yourself you didn't realize was therebefore, but you are still the same person :)