The score estimator is still very wrong and easy to fix for Japanese rules handicap games:
It’s confusing since Japanese rules specify no handicap compensation, but as long the counting is done with Chinese rules, the SE should apply compensation to get a count that corresponds closely to actual score.
Note that it does do the correct thing in Chinese rules games, so I think this fix just wasn’t applied correctly to all the rulesets.
I filed a bug report on GitHub too.