I play games with Japanese rules. The scoring at the end applies territory scoring which is what I would expect for Japanese rules. However, if during the game I choose “estimate score”, apparently the estimate score feature applies area scoring.
The estimate score option is just that - an estimate. I believe it uses area scoring because that allows for better estimates around midgame, when not s much is settled. Thus, groups that are more alive count for points, and groups that are not quite alive yet simply count for 0. I would recommend against using SE to determine if you’re winning, especially as you get stronger. Counting it yourself is always a better option.