I forked the game from here
and I think it’s better but still not quite right by default in Japanese rules.
The auto score does
but I would expect
which aligns better with the no points in seki.
It’s just normally you do have to play to remove these kinds of dead stones in a seki to gain points.
However I think, since it doesn’t count the underlying territory, maybe in this specific case it’s ok, because taking the one stone off the board by playing and taking it off in this way without giving anymore territory would score the same I think.
Possibly it would get a funny in between result when there’s two dead stones, which normally you can capture for three points - maybe I’ll try cook up a game board. ( Also just generally look at other game boards too 
)
I think the Chinese rules game looks good though
And the AGA area scoring one