Is there a way to change the Estimate Score function to use Japanese scoring? I’m a relatively new player, so my use of these terms might be wrong, but I believe the games I normally play are scored using Japanese rules, while the Estimate Score function uses Chinese scoring, which can be significantly different than Japanese scoring in certain scenarios.
I think that any difference between Japanese and Chinese scoring will most often be insignificant compared to the difference between the in-game score estimator and an accurate score estimation.
The in-game score estimator is flawed by design, because a very accurate score estimator would give too much computer aided assistence (which would amount to cheating).
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you can create custom games with Chinese rules or set prefer → Chinese in automatch settings, then no problem
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Area and Territory scoring gives the same result. The differences are
- 1 point if white passed first at the end of the game
- 1 point each time one player passes, but the other keeps playing. (This shouldn’t matter besides for beginner)
- eyes in seki: Seki is difficult for a computer to distinguish for an SE, so the SE would count eyes there probably anyways. In most cases the difference here is 0 or 1 point, Bigger differences are rare, if possible at all.
So there is no big differences, if any at all between different scoring methods.
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Just don’t use the ingame estimator 
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One huge difference is that SE assumes handicap stones being worth a point, thats good to remember when using it.
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Also the absolute numbers are very different even if the difference between the scores is the same or close. So it gives an impression of being very different even though it’s not.