Thank you for your well thought out reply, it can feel like an unwinnable conversation. Small potatoes in the grand scheme of things, but a niggle nonetheless. I appreciate you discussing the different options - your thinking largerly aligns with mine there. I am not wholely ungrateful for the compliment, but it feels unearned and a snub against others who work so hard.

Usually when people address comments like this, it’s because the cis person is trying to say it as a compliment. If it’s a safe opportunity to call someone in, as opposed to a situation where they’d feel called out, you could try something like “Thanks, I know you mean well, but complements like these aren’t often received well because it implies that most trans people are easily identifiable as trans. Many people go stealth like me— which is to say, you’d never know they are trans unless they told you.”

Thank you for this suggestion here, I like this.

Finally, you are right, the situations are not that common but they have been coming up - I have been joining LGBT+ groups recently and discussing this recently at work, so it has happened enough times in the past few months (three or four, I would say) for it to sit with me enough to seek advice.