I will do my best to answer, although I suspect all of us trans folk might respond differently.
I have two immediate thoughts. The first is that, although you might see it one way, most of us hear it in a different way. You seem to be implying that it is a form of validation, and I will admit to feeling validated when someone takes me for being cis. And at one point, that’s all I heard when someone said “I would never have known “ to me.
But something about it always felt uncomfortable. It was not until I examined the subtext that I realized what it was. The issue is that, despite what you mean to say, you are still implying that looking cis is some kind of norm and that I look like I fit that norm so well no one can tell I really don’t fit.
I know that’s not how you intend it, but consider this. If you were to discover someone you’ve known for a while was on the Autism spectrum, would you tell them you would never have known they had Autism? That’s only a compliment if the person is ashamed they are on the spectrum and trying to hide it. As someone with a spouse on the spectrum, doubt that would be the case for most people on the spectrum. The may not like being on the spectrum, but they don’t want to just blend in and pretend they aren’t, either, in my experience.
So that’s the main issue. Most of us feel as if we are hiding or that being trans is something to hide when someone says that. I don’t talk for everyone and, as I said, feel validated sometimes when, for instance, the nurse asks when was my last cycle. But I don’t feel good because I am trying to hide, I feel good because she immediately assumes I am a woman and treats me accordingly.
And I guess that’s the other issue. We just want to be treated like anyone else. I used to joke with a transgender friend about going up to non-trans people and telling them I would have never known they were cisgender. If I actually said that to someone, think of what it would imply: that being cis was somehow something to hide, that it was something people should not be able to tell if you are doing things right. In short, it others the cis person in this scenario.
I hope that was helpful to you. It was actually useful for me to be able to articulate just what bothers me about that phrase. Hopefully I did a good enough job of it that you can understand my perspective.