The game encourages scanning anomalies and using them to overcome planetary challenges, but this doesn't seem to be reflected in the score (eg marginal atmo with airtight caves still scores 250 for atmosphere, nothing for aesthetics or plants/animals). Any plans to adjust this?

No plans to adjust the scoring system this long after release. Things like airtight caves don't adjust your score directly, but they do make it more likely to have more colonists survive and get a better culture ending, so they do affect your score.

That makes sense, thanks for the quick reply.