If you believe the rest of the highly implausible theology of Christianity, you should be able to accept that the miracle of virgin birth included sourcing a Y chromosome from the same place they sourced an entire f-ing fetus.

Also, though trans people have always existed, the terminology you mentioned didn't. A lot of the lexicon is less than a decade old, and continues to evolve. And I mean, regardless, if Jesus were a trans man, or in other words a trans masc AFAB (assigned female at birth), his being referred to using he/him pronouns in the Bible, in conjunction with his presenting traditionally masculine, already tells you precisely how to interpret his gender.

This is how you should handle gendering trans people in general actually- when they clearly demonstrate to you by sharing/using their pronouns around you, or better yet they tell you outright what their gender is, regard them and refer to them as that gender. It's not something that's open to discussion; in fact it's quite inappropriate to do so. Each individual person is the one and only authority on what their gender is.

If you're ever in doubt, one question that IS appropriate to ask a trans person (or a cis person!) is, "what are your pronouns?". Even better, say, "hi, my name is _ and my pronouns are __. May I ask yours?". Boom. Easy.

Since you cant necessarily ask Jesus his pronouns, consider where you might have heard them already. Like when Jesus refers to himself as the son of God-that is a declaration of his gender right there, because he did not say daughter.

Hope this clears some things up for you. If not, im happy to answer any gender-related questions you may have, as a non-binary person myself, and/or try to answer any theology questions, though I have less experience, there.