I feel like you're overlooking probably the biggest hint Ben used when guessing your pronouns - namely, your body and face shape. Most people with penises look quite a bit different than people with vaginas, regardless of what they're wearing.

So although Ben didn't do a penis or DNA check, he still made a pretty educated guess that you had a penis, and decided, based on his assumption that you had a penis, that he was going to refer to you with he / him pronouns.

His choice of pronouns was still ultimately based on his assumption about your biology.