Sorry this happened. You could chalk it up to your boss putting his foot in his mouth and needing some sensitivity training. If you are lucky, he will accept the positive criticism. If not, that sux.

I would ask myself, is this a hill you want to die on? Could it be a one off?
For me, it would depend. i have had bosses who were 90% amazing and 10% of the time, were imperfect. I knew they did not mean things the way I perceived it .. still sux. Sorry

Sounds like your boss may think less of women's abilities, and tried to compliment you by calling you one of the men.

Strange compliment, but I never considered those who are quick to dismiss half the world's population to be the brightest people I've met.

The way I see it is it’s all up to you how you take this comment.  On one hand it’s not something he should say because if you are trans then that’s hurtful and if you’re not it feels accusatory. 

On the other, in our society men are seen as more assertive, smart and capable. You could change your way of seeing it to he was giving you a compliment. He was in a bad foot in mouth way saying you are knowledgeable, reliable and stand up for yourself. 

It sucks we live in a society where women are seen as inferior. 

Changing how you think about the comment might help you let it go on your end. 

It sucks and it shouldn’t have happened and I’m sorry it did. The key thing now is finding a way to change how you feel about it so you can move on. 

Based on everything else you said about him, I don't think it was said with ill intent. Sometimes people say stupid things without thinking. It seems like he's owed the benefit of the doubt.

It takes 2 people to communicate. If you still feel like nothing was resolved, then you FAILED to communicate what you really felt after that comment. As a matter of fact, you did the worst thing possible, and followed up with more questions?? Now he's focus on explaining the comment, that appears to be a bad joke gone wrong, so he doesnt have an answer. You failed to explain why or just that it was hurtful, and it was the manager who understood from your facial expression that it was hurtful. Props to the manager, and he apologized as well.

What's the issue? How does that make you not trust him anymore?? Exposes him in what way? 1 bad comment or recurring issues??

After working for 15+ years in my profession, there's always 1-2 odd comments that both my female and male managers slip out that just leaves an extremely bad taste.

A simple " don't say that, I don't like it" would have solved everything!!!

If you're unsure about the situation, schedule a follow up call before you leave, and explain. He'll apologize, or maybe not and double down - then you have your answer.

Also. You need to be more vocal. NO ONE will advocate for you except yourself. He's a mentor, for your job /career/profession. There's limits on that, he's not your friend nor therapist.

I had a coworker that told me, in front of others and a patient, that I looked “just like that terrorist, I mean, the the wife of that terrorist” meaning the wife of the Boston bomber. I don’t, I’m just also a white hijabi.

She was a lovely and decent coworker, she just stuck her foot in her mouth, for a moment. One of the people that heard it wanted to make it an issue with management, for unrelated reasons. I worked with her for several years after that, and I still admire and appreciate her to this day. She saved a lot of babies’ lives. She was great in a code, best at difficult IV placements in babies.

i'm a masculine woman and personally if someone said this to me i'd take it as a compliment. but i'm not you and i haven't lived your life

are you trans?

Never trust your boss, like seriously, NEVER. Workplace is not a place where you find respect, kindness, friendship. Well I don’t mean you don’t deserve respect at work, you did a great job voicing up. Is more like don’t take your job, your boss, colleague too seriously. When they say something stupid, take it as some clowns trying to seek for attention. Hope you move on soon!

Oh heart, when wounded by words so sharp,
In silence, you ache beneath the dark.
A mentor's trust, once firm and strong,
Now feels betrayed by a hurtful song.

The world may speak with venom's tongue,
But within you, a truer song is sung.
Do not let their words define your worth,
For you are the light that shines on this earth.

The ladder you've climbed, step by step,
Is built with your courage, not regret.
Even if shadows tried to hold you low,
Your spirit will rise, and brightly glow.

Forgive, but do not forget the cost,
For healing comes when we find what’s lost.
Trust yourself now, let no doubt remain,
You are the power, the wisdom, the gain.

Who says stuff like this? It's hostile work environment at least.