I feel like Samus’ true discomfort zone would be right in the middle of a big unfamiliar city
Yes, though I also think it depends on the city! She strikes me as introverted, so probably doesn't like long bursts in public spaces, but she may also be pretty curious (if scanning literally. every. detail is anything to go by- and thats canon because we all love doing it riiight?) so she might enjoy experiencing new cultures.
I think she'd be most uncomfortable in human-dominated urban areas, because they're busy and full of people specifically. Mixed-species places are better because there's such a variety anyway, but she might feel more like she stands out in a human environment, because of her Chozo upbringing and behaviours. She'd feel out of place, but also like she shouldn't feel that way because these are her people. It's not like she's some ordinary alien traveller who would understandably fail to get the local customs, because as a human she'd be expected to (even though human cultures themselves are highly varied- there's some things and behaviours that all humans roughly adhere to and Chozo might not, like body language and such).
In any case I think she'd want to keep her head low, avoid being recognised, and blend in with the crowd- this is probably easier to achieve in very mixed communities than in very human ones. Actually, late in her timeline, maybe she would be more comfortable in human cultures, having had plenty of time to adapt (being in the military among other humans probably helped) and maybe she actively wants to reconnect with the only people and homeworlds she has left.